From a08cf9481957889c8c246a4e15a8ed5bb32b31b7 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 18 Sep 2021 16:13:03 +0000 Subject: gnu: Add rust-barrel-0.6. * gnu/packages/crates-io.scm (rust-barrel-0.6): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 538e81338b..d9dfcc8bf5 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -4115,6 +4115,29 @@ trace (backtrace) at runtime in a Rust program.") (license (list license:asl2.0 license:expat)))) +(define-public rust-barrel-0.6 + (package + (name "rust-barrel") + (version "0.6.5") + (source + (origin + (method url-fetch) + (uri (crate-uri "barrel" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1qgzrfpp2acb06bbqrf5a8pjjwf3dwinq7sv2hqq0b1jn5wcjrwx")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-diesel" ,rust-diesel-1) + ("rust-tempfile" ,rust-tempfile-3)))) + (home-page "https://rust-db.github.io/barrel/") + (synopsis "Powerful schema migration building API for Rust") + (description "This package provides a powerful schema migration building +API for Rust.") + (license (list license:expat license:x11 license:asl2.0)))) + (define-public rust-base32-0.4 (package (name "rust-base32") -- cgit 1.4.1 From c4600ccebc968b34e7594ff426af02518418f574 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 18 Sep 2021 16:13:04 +0000 Subject: gnu: Add rust-strong-xml-derive-0.6. * gnu/packages/crates-io.scm (rust-strong-xml-derive-0.6): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index d9dfcc8bf5..ffca130454 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -47450,6 +47450,30 @@ and write it somewhere that does not easily support them, such as a log file.") (license (list license:asl2.0 license:expat)))) +(define-public rust-strong-xml-derive-0.6 + (package + (name "rust-strong-xml-derive") + (version "0.6.3") + (source + (origin + (method url-fetch) + (uri (crate-uri "strong-xml-derive" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1qf7smxaaglj7p9fs0csd0cyvwcy30w96pdy2aqi65ijk7s83iwj")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-proc-macro2" ,rust-proc-macro2-1) + ("rust-quote" ,rust-quote-1) + ("rust-syn" ,rust-syn-1)))) + (home-page "https://github.com/PoiScript/strong-xml") + (synopsis "Strong typed XML") + (description + "This package provides a strong typed XML parser, based on xmlparser.") + (license license:expat))) + (define-public rust-strsim-0.10 (package (name "rust-strsim") -- cgit 1.4.1 From 6893f4a9ac35a43bfb57e4103bc03a404bc45c49 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 18 Sep 2021 16:13:05 +0000 Subject: gnu: Add rust-debug-helper-0.3. * gnu/packages/crates-io.scm (rust-debug-helper-0.3): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index ffca130454..6016a0810a 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -13012,6 +13012,25 @@ sizes. Big-endian order is used. WARNING: Block must be aligned!") type.") (license (list license:expat license:asl2.0)))) +(define-public rust-debug-helper-0.3 + (package + (name "rust-debug-helper") + (version "0.3.12") + (source + (origin + (method url-fetch) + (uri (crate-uri "debug-helper" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1a73xl73psmzyihd62jy30g1acfmgjmyi2k8khmh170mrq6x3yvn")))) + (build-system cargo-build-system) + (home-page "https://magiclen.org/debug-helper") + (synopsis "Declarative macros to implement the Debug trait manually") + (description "This crate provides declarative macros to help you implement +the Debug trait manually.") + (license license:expat))) + (define-public rust-decimal-2 (package (name "rust-decimal") -- cgit 1.4.1 From ac99d1bb5924ea6977d58ea62d3ecd73f573332a Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 18 Sep 2021 16:13:06 +0000 Subject: gnu: Add rust-obfstr-0.3. * gnu/packages/crates-io.scm (rust-obfstr-0.3): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 6016a0810a..ede802363a 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -31192,6 +31192,28 @@ giga, kibi.") "This package can convert numbers into stack-allocated byte arrays.") (license (list license:expat license:asl2.0)))) +(define-public rust-obfstr-0.3 + (package + (name "rust-obfstr") + (version "0.3.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "obfstr" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0y5azgk8ds43m1sd5pc4hhakxzxkfcfscl24y8gsbvwdznxjqavv")))) + (arguments + `(#:rust ,rust-1.52)) ; fix for E0658 + (build-system cargo-build-system) + (home-page "https://github.com/CasualX/obfstr") + (synopsis "Compile time string constant obfuscation for Rust") + (description "This package provides a compile time string constant +obfuscation for Rust. The string constant itself is embedded in obfuscated +form and deobfuscated locally.") + (license license:expat))) + (define-public rust-obj-0.9 (package (name "rust-obj") -- cgit 1.4.1 From cfd3fbe35e74014c5d728642a2f7bc0ac4a36ad9 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 18 Sep 2021 16:13:07 +0000 Subject: gnu: Add rust-des-0.6. * gnu/packages/crates-io.scm (rust-des-0.6): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index ede802363a..d98c3cf786 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -13602,6 +13602,32 @@ traits for both structs and enums.") structs and enums.") (license license:expat))) +(define-public rust-des-0.6 + (package + (name "rust-des") + (version "0.6.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "des" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1bigk1x1kxvnfjn1alr8cc383z1flmj8q7g2pjl2zal8i1s7qkmj")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-byteorder" ,rust-byteorder-1) + ("rust-cipher" ,rust-cipher-0.2) + ("rust-opaque-debug" ,rust-opaque-debug-0.3)) + #:cargo-development-inputs + (("rust-cipher" ,rust-cipher-0.2)))) + (home-page "https://github.com/RustCrypto/block-ciphers") + (synopsis "DES and Triple DES block ciphers implementation") + (description "This package provides DES and Triple DES (3DES, TDES) block +ciphers implementations.") + (license (list license:expat license:asl2.0)))) + (define-public rust-deunicode-0.4 (package (name "rust-deunicode") -- cgit 1.4.1 From a2d73fc2478b3d5f721e2ee85d3fc5fc74e1bda2 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 18 Sep 2021 16:13:08 +0000 Subject: gnu: Add rust-entities-1. * gnu/packages/crates-io.scm (rust-entities-1): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index d98c3cf786..c8f3020f0c 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -15689,6 +15689,25 @@ Standard.") order.") (license license:expat))) +(define-public rust-entities-1 + (package + (name "rust-entities") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "entities" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1jnpr0zvj97wm9pnh7fnl74rzaar39hhg65p03cm08bqqgj0lcmm")))) + (build-system cargo-build-system) + (home-page "https://github.com/p-jackson/entities") + (synopsis "Raw data needed to convert to and from HTML entities") + (description "This package provides the raw data needed to convert to and +from HTML entities.") + (license license:expat))) + (define-public rust-enum-as-inner-0.3 (package (name "rust-enum-as-inner") -- cgit 1.4.1 From 55ac2e48cbb4f346a3f0e6860547a3660ef4bf23 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 18 Sep 2021 16:13:09 +0000 Subject: gnu: Add rust-escaper-0.1. * gnu/packages/crates-io.scm (rust-escaper-0.1): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index c8f3020f0c..1b74b2a476 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -16267,6 +16267,31 @@ deserialized from environment variables.") @code{no_std} environment.") (license license:boost1.0))) +(define-public rust-escaper-0.1 + (package + (name "rust-escaper") + (version "0.1.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "escaper" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0rhn3ipb5c3zns4wakclilfqzbmax6pwx7l367dipfj9fdxvjgm5")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-entities" ,rust-entities-1)) + #:cargo-development-inputs + (("rust-num" ,rust-num-0.4) + ("rust-rand" ,rust-rand-0.8)))) + (home-page "https://github.com/dignifiedquire/rust-escaper") + (synopsis "Library for HTML entity encoding and decoding") + (description "This package provides a library for HTML entity encoding and +decoding.") + (license (list license:asl2.0 license:expat license:mpl2.0)))) + (define-public rust-escargot-0.5 (package (name "rust-escargot") -- cgit 1.4.1 From 9116989d7876eb424c6e757d5e612ca6c74a47aa Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 18 Sep 2021 16:13:10 +0000 Subject: gnu: Add rust-crc-any-2. * gnu/packages/crates-io.scm (rust-crc-any-2): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 1b74b2a476..dc475bf307 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -10591,6 +10591,32 @@ to @code{is_x86_feature_detected}.") 64) with support for various standards.") (license (list license:expat license:asl2.0)))) +(define-public rust-crc-any-2 + (package + (name "rust-crc-any") + (version "2.3.12") + (source + (origin + (method url-fetch) + (uri (crate-uri "crc-any" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0fq85y5akcadahnj5nqbs47qhgp5cpfn2z19zc3gp4wpxr3989kr")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-debug-helper" ,rust-debug-helper-0.3) + ("rust-heapless" ,rust-heapless-0.5)) + #:cargo-development-inputs + (("rust-bencher" ,rust-bencher-0.1)))) + (home-page "https://magiclen.org/crc-any") + (synopsis "Compute CRC values") + (description "This package provides a crate to compute CRC values by +providing the length of bits, expression, reflection, an initial value and a +final xor value. It has many built-in CRC functions.") + (license license:expat))) + (define-public rust-crc32fast-1 (package (name "rust-crc32fast") -- cgit 1.4.1 From c918a0320043a81f66d794cea7aa04fc3572541f Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 18 Sep 2021 16:13:11 +0000 Subject: gnu: Add rust-tiger-0.1. * gnu/packages/crates-io.scm (rust-tiger-0.1): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index dc475bf307..d0dedd7859 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -50879,6 +50879,33 @@ fixed set of worker threads.") "You can bind to libsodium from Rust with this crate.") (license (list license:asl2.0 license:expat)))) +(define-public rust-tiger-0.1 + (package + (name "rust-tiger") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "tiger" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "01bhc7h8kxc5kjqx9sqrb3g8h4f9av6hpxzyihjq7pprphf56gj4")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-block-buffer" ,rust-block-buffer-0.9) + ("rust-byteorder" ,rust-byteorder-1) + ("rust-digest" ,rust-digest-0.9)) + #:cargo-development-inputs + (("rust-digest" ,rust-digest-0.9) + ("rust-hex-literal" ,rust-hex-literal-0.2)))) + (home-page "https://github.com/RustCrypto/hashes") + (synopsis "Tiger hash function") + (description + "This package provides the Tiger cryptographic hash function.") + (license (list license:expat license:asl2.0)))) + (define-public rust-tikv-jemalloc-sys-0.4 (package (name "rust-tikv-jemalloc-sys") -- cgit 1.4.1 From 7f0ccf82fa488989d067167e146b6243b21d5a27 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 18 Sep 2021 16:13:12 +0000 Subject: gnu: Add rust-libxml-0.3. * gnu/packages/crates-io.scm (rust-libxml-0.3): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index d0dedd7859..f54d1f3250 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -25566,6 +25566,37 @@ file. ("rust-pkg-config" ,rust-pkg-config-0.3) ("rust-vcpkg" ,rust-vcpkg-0.2)))))) +(define-public rust-libxml-0.3 + (package + (name "rust-libxml") + (version "0.3.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "libxml" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1f42qrc1mim85ivh2d4bn2wbqrn7dfg1i3l1q32yajcr835pxh02")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-libc" ,rust-libc-0.2) + ("rust-pkg-config" ,rust-pkg-config-0.3) + ("rust-vcpkg" ,rust-vcpkg-0.2)) + #:cargo-development-inputs + (("rust-criterion" ,rust-criterion-0.3) + ("rust-rayon" ,rust-rayon-1)))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("libxml2" ,libxml2))) + (home-page "https://github.com/KWARC/rust-libxml") + (synopsis "Rust wrapper for libxml2") + (description "This package provides a Rust wrapper for libxml2, the XML +C parser and toolkit developed for the GNOME project.") + (license license:expat))) + (define-public rust-libz-sys-1 (package (name "rust-libz-sys") -- cgit 1.4.1 From 6acc69ca52891dc0e3ba7c5eac95589bb82785f1 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 18 Sep 2021 16:13:13 +0000 Subject: gnu: Add rust-libxml-0.2. * gnu/packages/crates-io.scm (rust-libxml-0.2): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 14 ++++++++++++++ 1 file changed, 14 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index f54d1f3250..abd0ef75de 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -25597,6 +25597,20 @@ file. C parser and toolkit developed for the GNOME project.") (license license:expat))) +(define-public rust-libxml-0.2 + (package + (inherit rust-libxml-0.3) + (name "rust-libxml") + (version "0.2.17") + (source + (origin + (method url-fetch) + (uri (crate-uri "libxml" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1z567rqb55hxn0g7hpvcsh3nfvz9mdzlwk4mk179z9bkf7v10r29")))))) + (define-public rust-libz-sys-1 (package (name "rust-libz-sys") -- cgit 1.4.1 From 8a169eac59cc7b324710cfc74bdb897ad0c5e91f Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 18 Sep 2021 16:13:14 +0000 Subject: gnu: Add rust-article-scraper-1. * gnu/packages/crates-io.scm (rust-article-scraper-1): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index abd0ef75de..b36599a917 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -2433,6 +2433,46 @@ format.") ("rust-serde-derive" ,rust-serde-derive-1) ("rust-serde-json" ,rust-serde-json-1)))))) +(define-public rust-article-scraper-1 + (package + (name "rust-article-scraper") + (version "1.1.7") + (source + (origin + (method url-fetch) + (uri (crate-uri "article_scraper" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1l904hn99fgj83f3dhspxgz1j3xzgjbnbfsgvmhd1jg5l4hqfhxp")))) + (build-system cargo-build-system) + (arguments + `(#:tests? #f ;tests use the network + #:cargo-inputs + (("rust-base64" ,rust-base64-0.13) + ("rust-chrono" ,rust-chrono-0.4) + ("rust-encoding-rs" ,rust-encoding-rs-0.8) + ("rust-failure" ,rust-failure-0.1) + ("rust-image" ,rust-image-0.23) + ("rust-libxml" ,rust-libxml-0.2) + ("rust-log" ,rust-log-0.4) + ("rust-parking-lot" ,rust-parking-lot-0.11) + ("rust-regex" ,rust-regex-1) + ("rust-reqwest" ,rust-reqwest-0.11) + ("rust-tokio" ,rust-tokio-1) + ("rust-url" ,rust-url-2)))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("libxml2" ,libxml2) + ("openssl" ,openssl))) + (home-page "https://gitlab.com/news-flash/article_scraper") + (synopsis "Scrap article contents from the web") + (description "This package provides a crate to scrap article contents from +the web.") + ;; No copyright headers in the source code. LICENSE indicates gpl3. + (license license:gpl3))) + (define-public rust-askama-escape-0.10 (package (name "rust-askama-escape") -- cgit 1.4.1 From 54de80373d6931c1da18ba0cd8d4a092599117f3 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Wed, 3 Nov 2021 13:06:33 +0100 Subject: gnu: Add rust-feed-rs-0.6. * gnu/packages/crates-io.scm (rust-feed-rs-0.6): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index b36599a917..fa893df106 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -16897,6 +16897,37 @@ it.") descriptors limit.") (license license:asl2.0))) +(define-public rust-feed-rs-0.6 + (package + (name "rust-feed-rs") + (version "0.6.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "feed-rs" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1a1ain6r9k8bx7cz9pxqh3hdqbn8cqdkrbx78c8rxb7vqngyg53z")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-chrono" ,rust-chrono-0.4) + ("rust-lazy-static" ,rust-lazy-static-1) + ("rust-mime" ,rust-mime-0.3) + ("rust-quick-xml" ,rust-quick-xml-0.20) + ("rust-regex" ,rust-regex-1) + ("rust-serde" ,rust-serde-1) + ("rust-serde-json" ,rust-serde-json-1) + ("rust-siphasher" ,rust-siphasher-0.3) + ("rust-url" ,rust-url-2) + ("rust-uuid" ,rust-uuid-0.8)))) + (home-page "https://github.com/feed-rs/feed-rs") + (synopsis "Unified feed parser") + (description "This package provides a unified feed parser that handles +Atom, RSS 2.0, RSS 1.0, RSS 0.x and JSON Feed") + (license license:expat))) + (define-public rust-femme-2 (package (name "rust-femme") -- cgit 1.4.1 From 3e06ac60a031f15eb3b9a3ecd29ce9097b1c84d3 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 18 Sep 2021 16:13:16 +0000 Subject: gnu: Add rust-feedbin-api-0.1. * gnu/packages/crates-io.scm (rust-feedbin-api-0.1): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index fa893df106..b9a2e41ca2 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -16928,6 +16928,43 @@ descriptors limit.") Atom, RSS 2.0, RSS 1.0, RSS 0.x and JSON Feed") (license license:expat))) +(define-public rust-feedbin-api-0.1 + (package + (name "rust-feedbin-api") + (version "0.1.6") + (source + (origin + (method url-fetch) + (uri (crate-uri "feedbin-api" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "170xf3cgsqgqpnafpdmzzw9yvzc51r22lgr4f4hcrmidxlxpmlkp")))) + (build-system cargo-build-system) + (arguments + `(#:tests? #f ;tests use the network + #:cargo-inputs + (("rust-chrono" ,rust-chrono-0.4) + ("rust-failure" ,rust-failure-0.1) + ("rust-reqwest" ,rust-reqwest-0.11) + ("rust-serde" ,rust-serde-1) + ("rust-serde-derive" ,rust-serde-derive-1) + ("rust-serde-json" ,rust-serde-json-1) + ("rust-url" ,rust-url-2)) + #:cargo-development-inputs + (("rust-dotenv" ,rust-dotenv-0.15) + ("rust-rand" ,rust-rand-0.8) + ("rust-tokio" ,rust-tokio-1)))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("openssl" ,openssl))) + (home-page "https://gitlab.com/news-flash/feedbin_api") + (synopsis "Rust implementation of the Feedbin REST API") + (description + "This package provides a Rust implementation of the Feedbin REST API.") + (license license:unlicense))) + (define-public rust-femme-2 (package (name "rust-femme") -- cgit 1.4.1 From ab7b6199e321944f94daf19ff28eeb8a65762fa2 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 18 Sep 2021 16:13:17 +0000 Subject: gnu: Add rust-feedly-api-0.4. * gnu/packages/crates-io.scm (rust-feedly-api-0.4): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index b9a2e41ca2..928f17fe13 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -16965,6 +16965,46 @@ Atom, RSS 2.0, RSS 1.0, RSS 0.x and JSON Feed") "This package provides a Rust implementation of the Feedbin REST API.") (license license:unlicense))) +(define-public rust-feedly-api-0.4 + (package + (name "rust-feedly-api") + (version "0.4.7") + (source + (origin + (method url-fetch) + (uri (crate-uri "feedly-api" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1knad1bghc8hhfcyl35fcnhrk01vklamq07630rdk0pg6ax04swi")))) + (build-system cargo-build-system) + (arguments + `(#:tests? #f ;tests open external connections + #:cargo-inputs + (("rust-chrono" ,rust-chrono-0.4) + ("rust-failure" ,rust-failure-0.1) + ("rust-log" ,rust-log-0.4) + ("rust-percent-encoding" + ,rust-percent-encoding-2) + ("rust-reqwest" ,rust-reqwest-0.11) + ("rust-serde" ,rust-serde-1) + ("rust-serde-derive" ,rust-serde-derive-1) + ("rust-serde-json" ,rust-serde-json-1) + ("rust-url" ,rust-url-2)) + #:cargo-development-inputs + (("rust-dotenv" ,rust-dotenv-0.15) + ("rust-tokio" ,rust-tokio-1)))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("openssl" ,openssl))) + (home-page "https://gitlab.com/news-flash/feedly_api") + (synopsis "Rust implementation of the feedly REST API") + (description + "This package provides a Rust implementation of the feedly REST API.") + ;; No copyright headers in the source code. LICENSE indicates gpl3. + (license license:gpl3))) + (define-public rust-femme-2 (package (name "rust-femme") -- cgit 1.4.1 From 1e1c51a5e5095c20b9d7723c4b0509c5e79592fc Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 18 Sep 2021 16:13:18 +0000 Subject: gnu: Add rust-fever-api-0.2. * gnu/packages/crates-io.scm (rust-fever-api-0.2): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 928f17fe13..3cc1ba9e3e 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -17122,6 +17122,43 @@ Atom, RSS 2.0, RSS 1.0, RSS 0.x and JSON Feed") (("rust-clap" ,rust-clap-2) ("rust-tempdir" ,rust-tempdir-0.3)))))) +(define-public rust-fever-api-0.2 + (package + (name "rust-fever-api") + (version "0.2.11") + (source + (origin + (method url-fetch) + (uri (crate-uri "fever-api" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0pv4g241pc0bfwy9gjwsmrdv7mplzbifxr5mxf0k82yxawg55anc")))) + (build-system cargo-build-system) + (arguments + `(#:tests? #f ;tests use the network + #:cargo-inputs + (("rust-failure" ,rust-failure-0.1) + ("rust-log" ,rust-log-0.4) + ("rust-md5" ,rust-md5-0.7) + ("rust-reqwest" ,rust-reqwest-0.11) + ("rust-serde" ,rust-serde-1) + ("rust-serde-json" ,rust-serde-json-1) + ("rust-url" ,rust-url-2)) + #:cargo-development-inputs + (("rust-dotenv" ,rust-dotenv-0.15) + ("rust-tokio" ,rust-tokio-1)))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("openssl" ,openssl))) + (home-page "https://gitlab.com/news-flash/fever_api") + (synopsis "Rust implementation of the Fever API") + (description + "This packages provides a Rust implementation of the Fever API.") + ;; No copyright headers in the source code. LICENSE indicates gpl3. + (license license:gpl3))) + (define-public rust-filesize-0.2 (package (name "rust-filesize") -- cgit 1.4.1 From 209b27984d4f78be763a4e2cfc512c937e104b96 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Wed, 3 Nov 2021 13:08:41 +0100 Subject: gnu: Add rust-miniflux-api-0.3. * gnu/packages/crates-io.scm (rust-miniflux-api-0.3): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 3cc1ba9e3e..2c8fc5b5a2 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -28087,6 +28087,44 @@ file's MIME type by its extension.") ("rust-phf-codegen" ,rust-phf-codegen-0.7) ("rust-unicase" ,rust-unicase-1)))))) +(define-public rust-miniflux-api-0.3 + (package + (name "rust-miniflux-api") + (version "0.3.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "miniflux-api" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0r0bd907v2abv40i0c0xaj87ik4w9d3syn1f4byy0ssv55dw7mdq")))) + (build-system cargo-build-system) + (arguments + `(#:tests? #f ;tests use the network + #:cargo-inputs + (("rust-base64" ,rust-base64-0.13) + ("rust-failure" ,rust-failure-0.1) + ("rust-log" ,rust-log-0.4) + ("rust-reqwest" ,rust-reqwest-0.11) + ("rust-serde" ,rust-serde-1) + ("rust-serde-derive" ,rust-serde-derive-1) + ("rust-serde-json" ,rust-serde-json-1) + ("rust-url" ,rust-url-2)) + #:cargo-development-inputs + (("rust-dotenv" ,rust-dotenv-0.15) + ("rust-tokio" ,rust-tokio-1)))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("openssl" ,openssl))) + (home-page "https://gitlab.com/news-flash/miniflux_api") + (synopsis "Rust implementation of the Miniflux REST API") + (description + "This package provides a Rust implementation of the Miniflux REST API.") + ;; No copyright headers in the source code. LICENSE indicates gpl3. + (license license:gpl3))) + (define-public rust-minimal-lexical-0.1 (package (name "rust-minimal-lexical") -- cgit 1.4.1 From 614b4a8a42bc9df53c18a893dfed52764ae570c2 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 18 Sep 2021 16:13:20 +0000 Subject: gnu: Add rust-newsblur-api-0.1. * gnu/packages/crates-io.scm (rust-newsblur-api-0.1): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 2c8fc5b5a2..211822b99e 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -29819,6 +29819,41 @@ cryptographic library.") release (fork of debug_unreachable)") (license license:expat))) +(define-public rust-newsblur-api-0.1 + (package + (name "rust-newsblur-api") + (version "0.1.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "newsblur_api" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1lh5njrrk4fjc168npk1q3962dzsgmvz4fzvha46g9b83cf3jxzx")))) + (build-system cargo-build-system) + (arguments + `(#:tests? #f ;tests use the network + #:cargo-inputs + (("rust-failure" ,rust-failure-0.1) + ("rust-reqwest" ,rust-reqwest-0.11) + ("rust-serde" ,rust-serde-1) + ("rust-serde-json" ,rust-serde-json-1) + ("rust-url" ,rust-url-2)) + #:cargo-development-inputs + (("rust-dotenv" ,rust-dotenv-0.15) + ("rust-tokio" ,rust-tokio-1)))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("openssl" ,openssl))) + (home-page "https://gitlab.com/news-flash/newsblur_api/") + (synopsis "Rust implementation of the NewsBlur API") + (description + "This package provides a Rust implementation of the NewsBlur API.") + ;; No copyright headers in the source code. LICENSE indicates gpl3. + (license license:gpl3))) + (define-public rust-nibble-vec-0.1 (package (name "rust-nibble-vec") -- cgit 1.4.1 From 01de4d19a10e0051b0c3a11fb487494f039bdfe3 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 18 Sep 2021 16:13:21 +0000 Subject: gnu: Add rust-migrations-internals-1. * gnu/packages/crates-io.scm (rust-migrations-internals-1): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 211822b99e..8b08e259cd 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -27979,6 +27979,31 @@ quality, high performance hash algorithm.") "This package provides a simple math expression parser and evaluator.") (license (list license:unlicense license:expat)))) +(define-public rust-migrations-internals-1 + (package + (name "rust-migrations-internals") + (version "1.4.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "migrations_internals" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0q2qk4jpa16mcfcmhjz6hdg2s73az1k7j0cy08vvh87h997chkrb")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-barrel" ,rust-barrel-0.6) + ("rust-diesel" ,rust-diesel-1)) + #:cargo-development-inputs + (("rust-tempdir" ,rust-tempdir-0.3)))) + (home-page "https://diesel.rs") + (synopsis "Internal implementation of Diesel's migration mechanism") + (description "This package provides an internal implementation of Diesel's +migration mechanism.") + (license (list license:expat license:asl2.0)))) + (define-public rust-mimalloc-0.1 (package (name "rust-mimalloc") -- cgit 1.4.1 From 3970091d7f47b5bd2d9e4112e3a22469c80d27e4 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 18 Sep 2021 16:13:22 +0000 Subject: gnu: Add rust-migrations-macros-1. * gnu/packages/crates-io.scm (rust-migrations-macros-1): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 8b08e259cd..b91583c92b 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -28004,6 +28004,38 @@ quality, high performance hash algorithm.") migration mechanism.") (license (list license:expat license:asl2.0)))) +(define-public rust-migrations-macros-1 + (package + (name "rust-migrations-macros") + (version "1.4.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "migrations_macros" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "173qgwans6n2jf6b7qajq273rvg1r9c34p5fflzr53gx14lz2lwp")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-migrations-internals" + ,rust-migrations-internals-1) + ("rust-proc-macro2" ,rust-proc-macro2-1) + ("rust-quote" ,rust-quote-1) + ("rust-syn" ,rust-syn-1)) + #:cargo-development-inputs + (("rust-tempdir" ,rust-tempdir-0.3)))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("sqlite" ,sqlite))) + (home-page "https://diesel.rs") + (synopsis "Code generation macros for Diesel's embedded migrations") + (description "This package provides code generation macros for Diesel's +embedded migrations.") + (license (list license:expat license:asl2.0)))) + (define-public rust-mimalloc-0.1 (package (name "rust-mimalloc") -- cgit 1.4.1 From df7c90d1bc072f77b4cc08db1478fcfca21ab6c1 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 18 Sep 2021 17:03:19 +0000 Subject: gnu: Add rust-diesel-migrations-1. * gnu/packages/crates-io.scm (rust-diesel-migrations-1): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index b91583c92b..01b979ef34 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -13945,6 +13945,35 @@ Builder for PostgreSQL, SQLite, and MySQL.") Diesel.") (license (list license:expat license:asl2.0)))) +(define-public rust-diesel-migrations-1 + (package + (name "rust-diesel-migrations") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "diesel_migrations" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0k4g03ciqwya2xc1xvy5s9cs6q55k45wxa1gszswfg9m2f2dwg5z")))) + (build-system cargo-build-system) + (arguments + `(#:tests? #f ;doctest_setup.rs: No such file or directory + #:cargo-inputs + (("rust-migrations-internals" + ,rust-migrations-internals-1) + ("rust-migrations-macros" + ,rust-migrations-macros-1)) + #:cargo-development-inputs + (("rust-cfg-if" ,rust-cfg-if-0.1) + ("rust-diesel" ,rust-diesel-1) + ("rust-dotenv" ,rust-dotenv-0.10)))) + (home-page "https://diesel.rs") + (synopsis "Migration management for diesel") + (description "This package provides migration management for Diesel.") + (license (list license:expat license:asl2.0)))) + (define-public rust-diff-0.1 (package (name "rust-diff") -- cgit 1.4.1 From 00d5971a562a8f8fa6f6208d6c72ac80092f7b83 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 18 Sep 2021 17:03:21 +0000 Subject: gnu: Add rust-region-2. * gnu/packages/crates-io.scm (rust-region-2): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 01b979ef34..b0f0e9856c 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -39452,6 +39452,33 @@ uses finite automata and guarantees linear time matching on all inputs.") (("rust-quickcheck" ,rust-quickcheck-0.2) ("rust-rand" ,rust-rand-0.3)))))) +(define-public rust-region-2 + (package + (name "rust-region") + (version "2.2.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "region" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1q4szar3ms76552iygmhsvzhvvwkgz4l94qpx600vmyw5bm58zl7")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-bitflags" ,rust-bitflags-1) + ("rust-libc" ,rust-libc-0.2) + ("rust-mach" ,rust-mach-0.3) + ("rust-winapi" ,rust-winapi-0.3)) + #:cargo-development-inputs + (("rust-memmap" ,rust-memmap-0.7)))) + (home-page "https://github.com/darfink/region-rs") + (synopsis "Library for manipulating memory regions") + (description + "This package provides a library for manipulating memory regions.") + (license license:expat))) + (define-public rust-relative-path-1 (package (name "rust-relative-path") -- cgit 1.4.1 From 69d781ffaeae7ad0c73e520f95e77acfd344b02d Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 18 Sep 2021 17:03:24 +0000 Subject: gnu: Add rust-jetscii-0.5. * gnu/packages/crates-io.scm (rust-jetscii-0.5): New variable. (rust-jetscii-0.3): Inherit from above. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 33 ++++++++++++++++++++++++++------- 1 file changed, 26 insertions(+), 7 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index b0f0e9856c..2b35ad2fbf 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -24261,27 +24261,46 @@ primitives to an @code{io::Write}.") (native-inputs `(("jemalloc" ,jemalloc))))) -(define-public rust-jetscii-0.3 +(define-public rust-jetscii-0.5 (package (name "rust-jetscii") - (version "0.3.1") + (version "0.5.0") (source (origin (method url-fetch) (uri (crate-uri "jetscii" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "1sq6d6c9vi44gkr566w2f1d4n6mmrjx8gjdwgnhkgcsg051j391j")))) + (base32 "1x4z5ixlxv1wa70d3d6ad3n8qxz6z00i13zwnv219v45qcwybbnb")))) (build-system cargo-build-system) - (arguments `(#:skip-build? #t)) + (arguments + `(#:rust ,rust-1.52 ; fix for E0658 + #:cargo-development-inputs + (("rust-lazy-static" ,rust-lazy-static-1) + ("rust-memmap" ,rust-memmap-0.7) + ("rust-proptest" ,rust-proptest-1) + ("rust-region" ,rust-region-2)))) (home-page "https://github.com/shepmaster/jetscii") (synopsis "Search strings and byte slices for sets of ASCII characters or bytes") - (description - "This package provides a tiny library to efficiently search strings and -byte slices for sets of ASCII characters or bytes.") + (description "This package provides a tiny library to efficiently search +strings and byte slices for sets of ASCII characters or bytes.") (license license:expat))) +(define-public rust-jetscii-0.3 + (package + (inherit rust-jetscii-0.5) + (name "rust-jetscii") + (version "0.3.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "jetscii" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1sq6d6c9vi44gkr566w2f1d4n6mmrjx8gjdwgnhkgcsg051j391j")))) + (arguments `(#:skip-build? #t)))) + (define-public rust-jni-0.18 (package (name "rust-jni") -- cgit 1.4.1 From 17d7aeab49f2ca88b7d7b29756d92d2af9368bb6 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 18 Sep 2021 17:03:25 +0000 Subject: gnu: Add rust-strong-xml-0.6. * gnu/packages/crates-io.scm (rust-strong-xml-0.6): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 2b35ad2fbf..eb6e3bac60 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -48022,6 +48022,37 @@ and write it somewhere that does not easily support them, such as a log file.") (license (list license:asl2.0 license:expat)))) +(define-public rust-strong-xml-0.6 + (package + (name "rust-strong-xml") + (version "0.6.3") + (source + (origin + (method url-fetch) + (uri (crate-uri "strong-xml" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1gxy34j42x5a572cfkkhmxamrm764pswj5r3wcwi0bwfc4xgn68x")))) + (build-system cargo-build-system) + (arguments + `(#:rust ,rust-1.52 ; fix for E0658 + #:cargo-inputs + (("rust-jetscii" ,rust-jetscii-0.5) + ("rust-lazy-static" ,rust-lazy-static-1) + ("rust-log" ,rust-log-0.4) + ("rust-memchr" ,rust-memchr-2) + ("rust-strong-xml-derive" + ,rust-strong-xml-derive-0.6) + ("rust-xmlparser" ,rust-xmlparser-0.13)) + #:cargo-development-inputs + (("rust-env-logger" ,rust-env-logger-0.8)))) + (home-page "https://github.com/PoiScript/strong-xml") + (synopsis "Strong typed xml") + (description + "This package provides a strong typed XML parser, based on xmlparser.") + (license license:expat))) + (define-public rust-strong-xml-derive-0.6 (package (name "rust-strong-xml-derive") -- cgit 1.4.1 From e6c24b123f6662e627895c91f9cb85a3fb7e0a2b Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 18 Sep 2021 17:03:26 +0000 Subject: gnu: Add rust-opml-1. * gnu/packages/crates-io.scm (rust-opml-1): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index eb6e3bac60..2edd596a4f 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -32507,6 +32507,31 @@ system for OpenSSL.") "Extra FFI bindings to OpenSSL that require a C shim.") (license license:expat))) +(define-public rust-opml-1 + (package + (name "rust-opml") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "opml" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0zr7f101inkz3rknl0r3q0qkklfxhqrji7yxmqixajfn3m5mbjfa")))) + (build-system cargo-build-system) + (arguments + `(#:rust ,rust-1.52 ; fix for E0658 + #:cargo-inputs + (("rust-regex" ,rust-regex-1) + ("rust-serde" ,rust-serde-1) + ("rust-strong-xml" ,rust-strong-xml-0.6) + ("rust-thiserror" ,rust-thiserror-1)))) + (home-page "https://github.com/Holllo/opml") + (synopsis "OPML parser for Rust") + (description "This package provides an OPML parser for Rust.") + (license (list license:expat license:asl2.0)))) + (define-public rust-ord-subset-3 (package (name "rust-ord-subset") -- cgit 1.4.1 From 4b481835f2092358993e29ca73a434890b4fa27d Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 18 Sep 2021 17:03:27 +0000 Subject: gnu: Add rust-aes-soft-0.6. * gnu/packages/crates-io.scm (rust-aes-soft-0.6): New variable. (rust-aes-soft-0.4): Inherit from above. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 35 +++++++++++++++++++++++++++++------ 1 file changed, 29 insertions(+), 6 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 2edd596a4f..ad47029488 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -1274,21 +1274,21 @@ acceleration.") ("rust-subtle" ,rust-subtle-2) ("rust-zeroize" ,rust-zeroize-1)))))) -(define-public rust-aes-soft-0.4 +(define-public rust-aes-soft-0.6 (package (name "rust-aes-soft") - (version "0.4.0") + (version "0.6.4") (source (origin (method url-fetch) (uri (crate-uri "aes-soft" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 - "19szsg0qqxq42k7bj5p3svb147n8wxy9a20n4g7mcl2fwrz689a9")))) + (base32 "0wj0fi2pvmlw09yvb1aqf0mfkzrfxmjsf90finijh255ir4wf55y")))) (build-system cargo-build-system) (arguments - `(#:cargo-inputs + `(#:skip-build? #t + #:cargo-inputs (("rust-block-cipher" ,rust-block-cipher-0.7) ("rust-byteorder" ,rust-byteorder-1) ("rust-opaque-debug" ,rust-opaque-debug-0.2)) @@ -1297,9 +1297,32 @@ acceleration.") (home-page "https://github.com/RustCrypto/block-ciphers") (synopsis "Bit-sliced implementation of AES (Rijndael) block ciphers") (description "This package provides a bit-sliced implementation of -AES (Rijndael) block ciphers.") +AES (Rijndael) block ciphers. + +This package is deprecated and was replaced by the @code{aes} crate.") (license (list license:expat license:asl2.0)))) +(define-public rust-aes-soft-0.4 + (package + (inherit rust-aes-soft-0.6) + (name "rust-aes-soft") + (version "0.4.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "aes-soft" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "19szsg0qqxq42k7bj5p3svb147n8wxy9a20n4g7mcl2fwrz689a9")))) + (arguments + `(#:cargo-inputs + (("rust-block-cipher" ,rust-block-cipher-0.7) + ("rust-byteorder" ,rust-byteorder-1) + ("rust-opaque-debug" ,rust-opaque-debug-0.2)) + #:cargo-development-inputs + (("rust-block-cipher" ,rust-block-cipher-0.7)))))) + (define-public rust-aes-soft-0.3 (package (inherit rust-aes-soft-0.4) -- cgit 1.4.1 From edad11c2021a313989fb12821bb921cd4ea626fb Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 18 Sep 2021 17:03:28 +0000 Subject: gnu: Add rust-aesni-0.10. * gnu/packages/crates-io.scm (rust-aesni-0.10): New variable. (rust-aesni-0.7): Inherit from above. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 34 +++++++++++++++++++++++++++------- 1 file changed, 27 insertions(+), 7 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index ad47029488..a0660286f1 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -1342,8 +1342,34 @@ This package is deprecated and was replaced by the @code{aes} crate.") ("rust-byteorder" ,rust-byteorder-1) ("rust-opaque-debug" ,rust-opaque-debug-0.2)))))) +(define-public rust-aesni-0.10 + (package + (name "rust-aesni") + (version "0.10.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "aesni" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1kmh07fp9hbi1aa8dr2rybbgw8vqz6hjmk34c4w7sbscx7si2bpa")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-cipher" ,rust-cipher-0.2) + ("rust-opaque-debug" ,rust-opaque-debug-0.3)))) + (home-page "https://github.com/RustCrypto/block-ciphers") + (synopsis "AES (Rijndael) block ciphers implementation using AES-NI") + (description "This package provides an implementation of AES (Rijndael) +block ciphers using AES-NI. + +This package is deprecated and was replaced by the @code{aes} crate.") + (license (list license:expat license:asl2.0)))) + (define-public rust-aesni-0.7 (package + (inherit rust-aesni-0.10) (name "rust-aesni") (version "0.7.0") (source @@ -1354,7 +1380,6 @@ This package is deprecated and was replaced by the @code{aes} crate.") (sha256 (base32 "0r6j0mjkyqnwvgib01cvrwfw8rlx1biw75234niv723n1fdx6l6h")))) - (build-system cargo-build-system) (arguments `(#:cargo-inputs (("rust-block-cipher" ,rust-block-cipher-0.7) @@ -1362,12 +1387,7 @@ This package is deprecated and was replaced by the @code{aes} crate.") ("rust-stream-cipher" ,rust-stream-cipher-0.4)) #:cargo-development-inputs (("rust-block-cipher" ,rust-block-cipher-0.7) - ("rust-stream-cipher" ,rust-stream-cipher-0.4)))) - (home-page "https://github.com/RustCrypto/block-ciphers") - (synopsis "AES (Rijndael) block ciphers implementation using AES-NI") - (description "This package provides an implementation of AES (Rijndael) -block ciphers using AES-NI.") - (license (list license:expat license:asl2.0)))) + ("rust-stream-cipher" ,rust-stream-cipher-0.4)))))) (define-public rust-aesni-0.6 (package -- cgit 1.4.1 From a985851c9b635cc25a0fa0fbb553103a7cc828fd Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 18 Sep 2021 17:03:29 +0000 Subject: gnu: Add rust-aes-0.6. * gnu/packages/crates-io.scm (rust-aes-0.6): New variable. (rust-aes-0.4): Inherit from above. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 34 +++++++++++++++++++++++++++------- 1 file changed, 27 insertions(+), 7 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index a0660286f1..6e59f6b694 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -1173,8 +1173,34 @@ with Associated Data (AEAD) algorithms.") (("rust-generic-array" ,rust-generic-array-0.12) ("rust-heapless" ,rust-heapless-0.5)))))) +(define-public rust-aes-0.6 + (package + (name "rust-aes") + (version "0.6.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "aes" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0q85mw70mgr4glza9y9lrs9nxfa1cdcqzfk6wx0smb3623pr2hw8")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-aes-soft" ,rust-aes-soft-0.6) + ("rust-aesni" ,rust-aesni-0.10) + ("rust-cipher" ,rust-cipher-0.2)) + #:cargo-development-inputs + (("rust-cipher" ,rust-cipher-0.2)))) + (home-page "https://github.com/RustCrypto/block-ciphers") + (synopsis "Facade for AES (Rijndael) block ciphers implementations") + (description "This package provides a facade for AES (Rijndael) block +ciphers implementations.") + (license (list license:expat license:asl2.0)))) + (define-public rust-aes-0.4 (package + (inherit rust-aes-0.6) (name "rust-aes") (version "0.4.0") (source @@ -1185,19 +1211,13 @@ with Associated Data (AEAD) algorithms.") (sha256 (base32 "1xgsp2bn5llsppald60iw4497gaspslg0a8hknhniiz4zmki607p")))) - (build-system cargo-build-system) (arguments `(#:cargo-inputs (("rust-aes-soft" ,rust-aes-soft-0.4) ("rust-aesni" ,rust-aesni-0.7) ("rust-block-cipher" ,rust-block-cipher-0.7)) #:cargo-development-inputs - (("rust-block-cipher" ,rust-block-cipher-0.7)))) - (home-page "https://github.com/RustCrypto/block-ciphers") - (synopsis "Facade for AES (Rijndael) block ciphers implementations") - (description "This package provides a facade for AES (Rijndael) block -ciphers implementations.") - (license (list license:expat license:asl2.0)))) + (("rust-block-cipher" ,rust-block-cipher-0.7)))))) (define-public rust-aes-0.3 (package -- cgit 1.4.1 From 5fbac28da4f30f70c18f194cf31e32a41102ad84 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 18 Sep 2021 17:03:30 +0000 Subject: gnu: Add rust-block-modes-0.7. * gnu/packages/crates-io.scm (rust-block-modes-0.7): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 6e59f6b694..7d987c489b 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -5891,6 +5891,32 @@ algorithms. This package is deprecated. Please use block-cipher instead.") `(#:cargo-inputs (("rust-generic-array" ,rust-generic-array-0.8)))))) +(define-public rust-block-modes-0.7 + (package + (name "rust-block-modes") + (version "0.7.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "block-modes" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1w3jc3n7k4xq98b9mfina4wwpg1fq1s3b0mm5whqialb7q3yi82p")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-block-padding" ,rust-block-padding-0.2) + ("rust-cipher" ,rust-cipher-0.2)) + #:cargo-development-inputs + (("rust-aes" ,rust-aes-0.6) + ("rust-hex-literal" ,rust-hex-literal-0.2)))) + (home-page "https://github.com/RustCrypto/block-ciphers") + (synopsis "Block cipher modes of operation") + (description "This package provides a collection of block ciphers +and block modes.") + (license (list license:expat license:asl2.0)))) + (define-public rust-block-padding-0.2 (package (name "rust-block-padding") -- cgit 1.4.1 From d1b32323b782b0e44413511a102ecbc833ae833f Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 18 Sep 2021 17:03:31 +0000 Subject: gnu: Add rust-magic-crypt-3. * gnu/packages/crates-io.scm (rust-magic-crypt-3): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 7d987c489b..5e5e4213d1 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -26987,6 +26987,39 @@ Mach 3.0 kernel that underlies OSX.") library") (license (list license:asl2.0 license:expat)))) +(define-public rust-magic-crypt-3 + (package + (name "rust-magic-crypt") + (version "3.1.8") + (source + (origin + (method url-fetch) + (uri (crate-uri "magic-crypt" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1jb4m8wqxm2qkg9gcflxa0sg1d33a1a0r876h47njg43h494zjfk")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-aes-soft" ,rust-aes-soft-0.6) + ("rust-base64" ,rust-base64-0.13) + ("rust-block-modes" ,rust-block-modes-0.7) + ("rust-crc-any" ,rust-crc-any-2) + ("rust-des" ,rust-des-0.6) + ("rust-digest" ,rust-digest-0.9) + ("rust-md-5" ,rust-md-5-0.9) + ("rust-sha2" ,rust-sha2-0.9) + ("rust-tiger" ,rust-tiger-0.1)))) + (home-page "https://magiclen.org/aes") + (synopsis "Library for DES or AES encryption") + (description + "MagicCrypt is a library to encrypt/decrypt strings, files, or data, +using Data Encryption Standard(DES) or Advanced Encryption Standard(AES) +algorithms. It supports CBC block cipher mode, PKCS5 padding and 64, 128, +192 or 256-bits key length.") + (license license:asl2.0))) + (define-public rust-maildir-0.5 (package (name "rust-maildir") -- cgit 1.4.1 From 65234d0d3f384b1f5e24921168827d2628b1cd53 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 18 Sep 2021 17:03:32 +0000 Subject: gnu: Add rust-news-flash-1. * gnu/packages/crates-io.scm (rust-news-flash-1): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 72 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 72 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 5e5e4213d1..c76142bc58 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -30046,6 +30046,78 @@ cryptographic library.") release (fork of debug_unreachable)") (license license:expat))) +(define-public rust-news-flash-1 + (package + (name "rust-news-flash") + (version "1.2.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "news-flash" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0r3hz725kblxr6mhl8rkf2bffzmyya0ib3xr3jk5zm8x2jlpvlq6")))) + (build-system cargo-build-system) + (arguments + `(#:rust ,rust-1.52 ; some inputs fail with E0658 + #:tests? #f ; FIXME: "error reading DNS system conf" from reqwest + #:cargo-inputs + (("rust-article-scraper" ,rust-article-scraper-1) + ("rust-async-trait" ,rust-async-trait-0.1) + ("rust-base64" ,rust-base64-0.13) + ("rust-bitflags" ,rust-bitflags-1) + ("rust-bytes" ,rust-bytes-1) + ("rust-chrono" ,rust-chrono-0.4) + ("rust-diesel" ,rust-diesel-1) + ("rust-diesel-migrations" + ,rust-diesel-migrations-1) + ("rust-escaper" ,rust-escaper-0.1) + ("rust-failure" ,rust-failure-0.1) + ("rust-feed-rs" ,rust-feed-rs-0.6) + ("rust-feedbin-api" ,rust-feedbin-api-0.1) + ("rust-feedly-api" ,rust-feedly-api-0.4) + ("rust-fever-api" ,rust-fever-api-0.2) + ("rust-futures" ,rust-futures-0.3) + ("rust-hmac" ,rust-hmac-0.11) + ("rust-image" ,rust-image-0.23) + ("rust-itertools" ,rust-itertools-0.10) + ("rust-lazy-static" ,rust-lazy-static-1) + ("rust-libxml" ,rust-libxml-0.3) + ("rust-log" ,rust-log-0.4) + ("rust-magic-crypt" ,rust-magic-crypt-3) + ("rust-mime" ,rust-mime-0.3) + ("rust-mime-guess" ,rust-mime-guess-2) + ("rust-miniflux-api" ,rust-miniflux-api-0.3) + ("rust-newsblur-api" ,rust-newsblur-api-0.1) + ("rust-obfstr" ,rust-obfstr-0.3) + ("rust-opml" ,rust-opml-1) + ("rust-parking-lot" ,rust-parking-lot-0.11) + ("rust-rayon" ,rust-rayon-1) + ("rust-regex" ,rust-regex-1) + ("rust-reqwest" ,rust-reqwest-0.11) + ("rust-rust-embed" ,rust-rust-embed-5) + ("rust-serde" ,rust-serde-1) + ("rust-serde-derive" ,rust-serde-derive-1) + ("rust-serde-json" ,rust-serde-json-1) + ("rust-sha-1" ,rust-sha-1-0.9) + ("rust-url" ,rust-url-2)) + #:cargo-development-inputs + (("rust-tempfile" ,rust-tempfile-3) + ("rust-tokio" ,rust-tokio-1)))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("libxml2" ,libxml2) + ("openssl" ,openssl) + ("sqlite" ,sqlite))) + (home-page "https://gitlab.com/news-flash/news_flash") + (synopsis "Base library for NewsFlash") + (description "This package provides the base library for the NewsFlash +feed reader.") + ;; No copyright headers in the source code. LICENSE indicates gpl3. + (license license:gpl3))) + (define-public rust-newsblur-api-0.1 (package (name "rust-newsblur-api") -- cgit 1.4.1 From f19e11e1da183dddb8921c7778bca5a12e42daf8 Mon Sep 17 00:00:00 2001 From: David Larsson Date: Tue, 26 Oct 2021 19:39:37 +0200 Subject: gnu: Add python-sqlalchemy@1.3. * gnu/packages/databases.scm (python-sqlalchemy-1.3): New variable. Signed-off-by: Tobias Geerinckx-Rice --- gnu/packages/databases.scm | 12 ++++++++++++ 1 file changed, 12 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 0da6c2d1be..7fcdacce7c 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -3006,6 +3006,18 @@ designed for efficient and high-performing database access, adapted into a simple and Pythonic domain language.") (license license:x11))) +(define-public python-sqlalchemy-1.3 + (package + (inherit python-sqlalchemy) + (version "1.3.20") + (source + (origin + (method url-fetch) + (uri (pypi-uri "SQLAlchemy" version)) + (sha256 + (base32 "18b9am7bsqc4nj3d2h5r93i002apczxfvpfpcqbd6f0385zmrwnj")))) + (propagated-inputs '()))) + (define-public python2-sqlalchemy (package-with-python2 python-sqlalchemy)) -- cgit 1.4.1 From 64835a71034eb256dc9426cf6080286596812be5 Mon Sep 17 00:00:00 2001 From: David Larsson Date: Tue, 26 Oct 2021 19:44:35 +0200 Subject: gnu: Add python-marshmallow@3.2. * gnu/packages/python-xyz.scm (python-marshmallow-3.2): New variable. Signed-off-by: Tobias Geerinckx-Rice --- gnu/packages/python-xyz.scm | 11 +++++++++++ 1 file changed, 11 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 32d6b403d4..8dd10d39af 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19168,6 +19168,17 @@ Python datatypes.") complex datatypes to and from native Python datatypes.") (license license:expat))) +(define-public python-marshmallow-3.2 + (package + (inherit python-marshmallow) + (version "3.2.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "marshmallow" version)) + (sha256 + (base32 "1w18klwj0z9bqxj252qpj1hz8l46nl27sbc89rkajc7mln73wbws")))))) + (define-public python-apispec (package (name "python-apispec") -- cgit 1.4.1 From 62820800cb3a8852c0b7b1015486859508f09cbf Mon Sep 17 00:00:00 2001 From: David Larsson Date: Tue, 26 Oct 2021 19:51:50 +0200 Subject: gnu: Add python-marshmallow-jsonapi. * gnu/packages/python-xyz.scm (python-marshmallow-jsonapi): New variable. Signed-off-by: Tobias Geerinckx-Rice --- gnu/packages/python-xyz.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 8dd10d39af..403143fd6d 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19179,6 +19179,36 @@ complex datatypes to and from native Python datatypes.") (sha256 (base32 "1w18klwj0z9bqxj252qpj1hz8l46nl27sbc89rkajc7mln73wbws")))))) +(define-public python-marshmallow-jsonapi + (package + (name "python-marshmallow-jsonapi") + (version "0.24.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "marshmallow-jsonapi" version)) + (sha256 + (base32 "1d9pxcgmln4gls99vwj1h24qv0lz7fb2jqmqrsiv1pid1snc125x")))) + (build-system python-build-system) + (propagated-inputs + `(("python-marshmallow" ,python-marshmallow-3.2))) + (native-inputs + `(("python-faker" ,python-faker) + ("python-flake8" ,python-flake8) + ("python-flake8-bugbear" ,python-flake8-bugbear) + ("python-flask" ,python-flask) + ("python-mock" ,python-mock) + ("python-pre-commit" ,python-pre-commit) + ("python-pytest" ,python-pytest) + ("python-tox" ,python-tox))) + (home-page "https://github.com/marshmallow-code/marshmallow-jsonapi") + (synopsis "JSON:API 1.0 formatting with Marshmallow") + (description + "The marshmallow-jsonapi package provides a simple way to produce +@uref{https://jsonapi.org, JSON:API}-compliant data in any Python Web framework. +It includes optional utilities to integrate with Flask.") + (license license:expat))) + (define-public python-apispec (package (name "python-apispec") -- cgit 1.4.1 From 52a7fba8fc78763967c15781ea9b9176d3b4cc26 Mon Sep 17 00:00:00 2001 From: David Larsson Date: Wed, 27 Oct 2021 09:04:40 +0200 Subject: gnu: Add python-flask-combo-jsonapi. * gnu/packages/python-web.scm (python-flask-combo-jsonapi): New variable. Signed-off-by: Tobias Geerinckx-Rice --- gnu/packages/python-web.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 8a72f33a91..a37681dab4 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -6251,3 +6251,42 @@ communicate with Microsoft Azure Storage services.") comments, or tags from HTML snippets, extract base url from HTML snippets, translate entities on HTML strings, among other things.") (license license:bsd-3))) + +(define-public python-flask-combo-jsonapi + (package + (name "python-flask-combo-jsonapi") + (version "1.1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/AdCombo/flask-combo-jsonapi") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "07fhcjiyif80z1vyh35za29sqx1mmqh568jrbrrs675j4a797sj1")))) + (build-system python-build-system) + (propagated-inputs + `(("python-flask" ,python-flask) + ("python-marshmallow" ,python-marshmallow-3.2) + ("python-marshmallow-jsonapi" ,python-marshmallow-jsonapi) + ("python-simplejson" ,python-simplejson) + ("python-sqlalchemy" ,python-sqlalchemy-1.3) + ("python-apispec" ,python-apispec) + ("python-simplejson" ,python-simplejson) + ("python-six" ,python-six))) + (native-inputs + `(("python-coverage" ,python-coverage) + ("python-coveralls" ,python-coveralls) + ("python-pytest" ,python-pytest) + ("python-pytest-runner" ,python-pytest-runner))) + (home-page "https://github.com/AdCombo/flask-combo-jsonapi") + (synopsis "Flask extension to quickly create JSON:API 1.0 REST Web APIs") + (description + "Flask-COMBO-JSONAPI is a Python Flask extension for building REST Web APIs +compliant with the @uref{https://jsonapi.org, JSON:API 1.0} specification. + +It tries to combine the power of Flask-Restless with the flexibility of +Flask-RESTful to quickly build APIs that fit the complexity of existing +real-life projects with legacy data and diverse storage providers.") + (license license:expat))) -- cgit 1.4.1 From ccb2fabee0c0d71808a9e0c90db3f8f0f43c803f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 3 Nov 2021 15:06:48 +0100 Subject: gnu: python-sqlalchemy: Update to 1.4.26. * gnu/packages/databases.scm (python-sqlalchemy): Update to 1.4.26. --- gnu/packages/databases.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 7fcdacce7c..0404f63684 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -2977,13 +2977,13 @@ Database API 2.0T.") (define-public python-sqlalchemy (package (name "python-sqlalchemy") - (version "1.4.23") + (version "1.4.26") (source (origin (method url-fetch) (uri (pypi-uri "SQLAlchemy" version)) (sha256 - (base32 "10vm8hm8w4yfsab076ak8r4vp5v1jqdi71cky6dhha7mh5l29zvn")))) + (base32 "06imr96jirwmkc8mkxrl9bi413yd3638lc5idn65xx8fv7bzkivb")))) (build-system python-build-system) (native-inputs `(("python-cython" ,python-cython) ; for C extensions -- cgit 1.4.1 From 23489e69f29cf4f2794f4a2180a9aca01567585a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 3 Nov 2021 15:08:18 +0100 Subject: gnu: python-sqlalchemy: Respect #:tests?. * gnu/packages/databases.scm (python-sqlalchemy)[argument]: Respect the #:tests? keyword in the custom 'check phase. --- gnu/packages/databases.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 0404f63684..e1d639f86b 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -2995,7 +2995,9 @@ Database API 2.0T.") `(#:phases (modify-phases %standard-phases (replace 'check - (lambda _ (invoke "py.test")))))) + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "py.test"))))))) (home-page "https://www.sqlalchemy.org") (synopsis "Database abstraction library") (description -- cgit 1.4.1 From 6259bfab86f77c397764c06562b2917bb552d196 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 3 Nov 2021 15:19:13 +0100 Subject: gnu: python-marshmallow: Fix linter warning. * gnu/packages/python-xyz.scm (python-marshmallow)[synopsis]: Drop the full stop. --- gnu/packages/python-xyz.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 403143fd6d..8ba72170c0 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19163,7 +19163,7 @@ address is valid and really exists.") ("python-pytz" ,python-pytz))) (home-page "https://github.com/marshmallow-code/marshmallow") (synopsis "Convert complex datatypes to and from native -Python datatypes.") +Python datatypes") (description "@code{marshmallow} provides a library for converting complex datatypes to and from native Python datatypes.") (license license:expat))) -- cgit 1.4.1 From fc871847f67eb7d2a55c6db84d9e9166af71b501 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 3 Nov 2021 15:23:28 +0100 Subject: gnu: ghc-persistent: Curate storage system examples. * gnu/packages/haskell-xyz.scm (ghc-persistent)[description]: Choose better-licenced storage system examples. --- gnu/packages/haskell-xyz.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/haskell-xyz.scm b/gnu/packages/haskell-xyz.scm index 6fb6933be4..ae077f7400 100644 --- a/gnu/packages/haskell-xyz.scm +++ b/gnu/packages/haskell-xyz.scm @@ -9874,8 +9874,7 @@ syntax and semantics as Perl 5.") (home-page "https://www.yesodweb.com/book/persistent") (synopsis "Type-safe, multi-backend data serialization for Haskell") (description "This Haskell package allows Haskell programs to access data -storage systems like PostgreSQL, SQLite, MySQL and MongoDB in a type-safe -way.") +storage systems like PostgreSQL, SQLite, and MariaDB in a type-safe way.") (license license:expat))) (define-public ghc-persistent-sqlite -- cgit 1.4.1 From 64753a7bc5c3b2c958706e6a7d08e34db24008cf Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 3 Nov 2021 15:27:37 +0100 Subject: gnu: unqlite: Curate comparisons. * gnu/packages/databases.scm (unqlite)[description]: Keep the better-licenced comparisons. --- gnu/packages/databases.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index e1d639f86b..92a7aa2761 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -2214,7 +2214,7 @@ easy, requiring concise and simple code.") "UnQLite is an in-process software library which implements a self-contained, serverless, zero-configuration, transactional NoSQL database engine. UnQLite is a document store database similar to -MongoDB, Redis, CouchDB, etc. as well as a standard Key/Value store +Redis, CouchDB, etc., as well as a standard key/value store similar to BerkeleyDB, LevelDB, etc.") (license license:bsd-2))) -- cgit 1.4.1 From d5833914cfefbfb95683ed3e5160553399cc9d3d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 3 Nov 2021 16:35:36 +0100 Subject: gnu: snd: Update to 4.3.8. * gnu/packages/dns.scm (snd): Update to 4.3.8. [arguments]: Don't explicitly return #t from phases. --- gnu/packages/dns.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm index 89ebe588fd..75bea46e23 100644 --- a/gnu/packages/dns.scm +++ b/gnu/packages/dns.scm @@ -592,14 +592,14 @@ asynchronous fashion.") (define-public nsd (package (name "nsd") - (version "4.3.7") + (version "4.3.8") (source (origin (method url-fetch) (uri (string-append "https://www.nlnetlabs.nl/downloads/nsd/nsd-" version ".tar.gz")) (sha256 - (base32 "1bg87g0i66hw16fm7gbqmzyi2rcn1hadzz0bg9b8s5mx7g2rwfzx")))) + (base32 "1qcrrglm3r486r6n26h5fr1xb1k8jf63gm9b43wrhnigywjpx28i")))) (build-system gnu-build-system) (arguments `(#:configure-flags @@ -635,8 +635,7 @@ asynchronous fashion.") ((".*INSTALL.*\\$\\((config|pid|xfr|db)dir" command) (string-append "#" command)) (("\\$\\(nsdconfigfile\\)\\.sample" file-name) - (string-append doc "/examples/" file-name))) - #t)))) + (string-append doc "/examples/" file-name))))))) #:tests? #f)) ; no tests (inputs `(("libevent" ,libevent) -- cgit 1.4.1 From 9b917c2615d8a03bcced6d453d8e5d3020da7d6b Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 3 Nov 2021 16:35:46 +0100 Subject: gnu: knot: Update to 3.1.3. * gnu/packages/dns.scm (knot): Update to 3.1.3. --- gnu/packages/dns.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm index 75bea46e23..0aaa22bbfd 100644 --- a/gnu/packages/dns.scm +++ b/gnu/packages/dns.scm @@ -923,7 +923,7 @@ Extensions} (DNSSEC).") (define-public knot (package (name "knot") - (version "3.1.2") + (version "3.1.3") (source (origin (method git-fetch) @@ -932,7 +932,7 @@ Extensions} (DNSSEC).") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1kyjf6d1jx8q0zjzwy06f4d3ar5cbbqxka8cc7ckwmbpf1n6cij5")) + (base32 "19hm17r6v8p9k3jp3bkj4xzjrb8irfmpgz6mjad5gfhmgr4pmi51")) (modules '((guix build utils))) (snippet '(begin -- cgit 1.4.1 From 5c1ad6b9247a0c8e04add9331ffd8aec6a5e4ddf Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 3 Nov 2021 18:44:02 +0100 Subject: gnu: libblockdev: Update to 2.26. * gnu/packages/disk.scm (libblockdev): Update to 2.26. [source]: Remove patch. * gnu/packages/patches/libblockdev-glib-compat.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/disk.scm | 5 +- gnu/packages/patches/libblockdev-glib-compat.patch | 61 ---------------------- 3 files changed, 2 insertions(+), 65 deletions(-) delete mode 100644 gnu/packages/patches/libblockdev-glib-compat.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index 5ae09d7d57..05258ac054 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1333,7 +1333,6 @@ dist_patch_DATA = \ %D%/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch \ %D%/packages/patches/julia-tracker-16-compat.patch \ %D%/packages/patches/kdbusaddons-kinit-file-name.patch \ - %D%/packages/patches/libblockdev-glib-compat.patch \ %D%/packages/patches/libffi-3.3-powerpc-fixes.patch \ %D%/packages/patches/libffi-float128-powerpc64le.patch \ %D%/packages/patches/libvirt-add-install-prefix.patch \ diff --git a/gnu/packages/disk.scm b/gnu/packages/disk.scm index abe49d7ad3..c457bfd1bf 100644 --- a/gnu/packages/disk.scm +++ b/gnu/packages/disk.scm @@ -923,16 +923,15 @@ to create devices with respective mappings for the ATARAID sets discovered.") (define-public libblockdev (package (name "libblockdev") - (version "2.25") + (version "2.26") (source (origin (method url-fetch) (uri (string-append "https://github.com/storaged-project/" "libblockdev/releases/download/" version "-1/libblockdev-" version ".tar.gz")) - (patches (search-patches "libblockdev-glib-compat.patch")) (sha256 (base32 - "0s0nazkpzpn4an00qghjkk9n7gdm5a8dqfr5hfnlk5mk5lma8njm")))) + "0sg068jb87ljhn8yazrqxi6ri10ic2sh1lp6ikd2nqxc6l5y3h64")))) (build-system gnu-build-system) (arguments `(#:phases diff --git a/gnu/packages/patches/libblockdev-glib-compat.patch b/gnu/packages/patches/libblockdev-glib-compat.patch deleted file mode 100644 index bb25d5d963..0000000000 --- a/gnu/packages/patches/libblockdev-glib-compat.patch +++ /dev/null @@ -1,61 +0,0 @@ -Don't use g_memdup() which is removed in newer versions of GLib. - -See . - -Taken from upstream: -https://github.com/storaged-project/libblockdev/commit/5528baef6ccc835a06c45f9db34a2c9c3f2dd940 - -diff --git a/src/lib/plugin_apis/vdo.api b/src/lib/plugin_apis/vdo.api ---- a/src/lib/plugin_apis/vdo.api -+++ b/src/lib/plugin_apis/vdo.api -@@ -170,7 +170,22 @@ void bd_vdo_stats_free (BDVDOStats *stats) { - * Deprecated: 2.24: Use LVM-VDO integration instead. - */ - BDVDOStats* bd_vdo_stats_copy (BDVDOStats *stats) { -- return g_memdup (stats, sizeof (BDVDOStats)); -+ if (stats == NULL) -+ return NULL; -+ -+ BDVDOStats *new_stats = g_new0 (BDVDOStats, 1); -+ -+ new_stats->block_size = stats->block_size; -+ new_stats->logical_block_size = stats->logical_block_size; -+ new_stats->physical_blocks = stats->physical_blocks; -+ new_stats->data_blocks_used = stats->data_blocks_used; -+ new_stats->overhead_blocks_used = stats->overhead_blocks_used; -+ new_stats->logical_blocks_used = stats->logical_blocks_used; -+ new_stats->used_percent = stats->used_percent; -+ new_stats->saving_percent = stats->saving_percent; -+ new_stats->write_amplification_ratio = stats->write_amplification_ratio; -+ -+ return new_stats; - } - - GType bd_vdo_stats_get_type () { -diff --git a/src/plugins/vdo.c b/src/plugins/vdo.c ---- a/src/plugins/vdo.c -+++ b/src/plugins/vdo.c -@@ -81,7 +81,22 @@ void bd_vdo_stats_free (BDVDOStats *stats) { - } - - BDVDOStats* bd_vdo_stats_copy (BDVDOStats *stats) { -- return g_memdup (stats, sizeof (BDVDOStats)); -+ if (stats == NULL) -+ return NULL; -+ -+ BDVDOStats *new_stats = g_new0 (BDVDOStats, 1); -+ -+ new_stats->block_size = stats->block_size; -+ new_stats->logical_block_size = stats->logical_block_size; -+ new_stats->physical_blocks = stats->physical_blocks; -+ new_stats->data_blocks_used = stats->data_blocks_used; -+ new_stats->overhead_blocks_used = stats->overhead_blocks_used; -+ new_stats->logical_blocks_used = stats->logical_blocks_used; -+ new_stats->used_percent = stats->used_percent; -+ new_stats->saving_percent = stats->saving_percent; -+ new_stats->write_amplification_ratio = stats->write_amplification_ratio; -+ -+ return new_stats; - } - - -- cgit 1.4.1 From 095b76c2547a92b506c4b55a425d067580c7c9c4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:47:28 +0000 Subject: gnu: r-interval: Update to 1.1-0.8. * gnu/packages/bioconductor.scm (r-interval): Update to 1.1-0.8. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 90a0e1f288..75f6c877b4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12222,14 +12222,14 @@ truncated data.") (define-public r-interval (package (name "r-interval") - (version "1.1-0.7") + (version "1.1-0.8") (source (origin (method url-fetch) (uri (cran-uri "interval" version)) (sha256 (base32 - "1b31lh0sv7lzy76230djipahxa10lblbr37kdiigr6hp3dd1xmz9")))) + "0g0k9nri19p3y3s70ic1w3i3sxq8fbsxaikd7c4d6afqzr8hk2nl")))) (properties `((upstream-name . "interval"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From bf379a9d5e8b05386c7889fee179ba6b3a9cd64d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:13 +0000 Subject: gnu: r-datawizard: Update to 0.2.1. * gnu/packages/cran.scm (r-datawizard): Update to 0.2.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5384dbcb29..21068ba7f7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -187,14 +187,14 @@ etc.") (define-public r-datawizard (package (name "r-datawizard") - (version "0.2.0.1") + (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "datawizard" version)) (sha256 (base32 - "15q491qix4a9b10wkb5bm9jnnr62smjw4qdrw4bd51i1kgvd6kl5")))) + "062phzfcvn79npn4s58gz1m5ignyvr4q2zlqnyxla4p7l760djl9")))) (properties `((upstream-name . "datawizard"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 909d67f4098e528ff3fd28026ae90767290de06e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:13 +0000 Subject: gnu: r-diffobj: Update to 0.3.5. * gnu/packages/cran.scm (r-diffobj): Update to 0.3.5. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 21068ba7f7..2b5e8c9aa4 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -212,14 +212,14 @@ wrangling backend for the packages in the @code{easystats} ecosystem.") (define-public r-diffobj (package (name "r-diffobj") - (version "0.3.4") + (version "0.3.5") (source (origin (method url-fetch) (uri (cran-uri "diffobj" version)) (sha256 (base32 - "1z4yhfasjpi9rxl1lh9bny7yvs947a6hhc768azc1wwad748mk9q")))) + "0q6gwd9pqh41f6j5p9jl92aji4p8kx9inffpha93d7jc3ndsfq6q")))) (properties `((upstream-name . "diffobj"))) (build-system r-build-system) (propagated-inputs `(("r-crayon" ,r-crayon))) -- cgit 1.4.1 From c9cb6170bcdedd3229a59c081c0e582ab12dae93 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:14 +0000 Subject: gnu: r-rvest: Update to 1.0.2. * gnu/packages/cran.scm (r-rvest): Update to 1.0.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2b5e8c9aa4..e22b7fa23e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1232,13 +1232,13 @@ single step.") (define-public r-rvest (package (name "r-rvest") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "rvest" version)) (sha256 - (base32 "1v99bpp2077s4y5phvkzpgjyr8cs9axifm1c3npw6jmh8x9j91h8")))) + (base32 "1905vxgnj3q09l1wf6rwxpbpydznp06nbkrclnc05j2415z4gfw9")))) (build-system r-build-system) (propagated-inputs `(("r-httr" ,r-httr) -- cgit 1.4.1 From 88b359ab0eedef6f8df8270e5abd854ab0456aec Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:14 +0000 Subject: gnu: r-htmltable: Update to 2.3.0. * gnu/packages/cran.scm (r-htmltable): Update to 2.3.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e22b7fa23e..eb85f9e3f6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1685,13 +1685,13 @@ applications.") (define-public r-htmltable (package (name "r-htmltable") - (version "2.2.1") + (version "2.3.0") (source (origin (method url-fetch) (uri (cran-uri "htmlTable" version)) (sha256 - (base32 "05zy9acx4s80dr880q69i4rcjqgmbz18gn7pyazda9gsnm981j96")))) + (base32 "0xx5fza40six81mkfjsja6a8j6cg1mlzg0cxfgv084riyq79l387")))) (properties `((upstream-name . "htmlTable"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From bce8638f0656d033e69772faf2cbbfec9c54c2b6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:14 +0000 Subject: gnu: r-bslib: Update to 0.3.1. * gnu/packages/cran.scm (r-bslib): Update to 0.3.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index eb85f9e3f6..6ac81d7c6a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1972,14 +1972,14 @@ language, which is stable, powerful, and CSS compatible.") (define-public r-bslib (package (name "r-bslib") - (version "0.3.0") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "bslib" version)) (sha256 (base32 - "0zfjavz5jw4lfbrmc3rgsivcrxq2ia9jwmfbcrdxnxlmyri8qinr")) + "0jcqklry1nkibz0sydsz5xdsnb4wnrrhvmyr9ji3k45bbipbap2z")) (snippet '(for-each delete-file '("inst/lib/bs-a11y-p/plugins/js/bootstrap-accessibility.min.js" -- cgit 1.4.1 From d4c9449f121dab6239d64befc16ce083935fe8f6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:15 +0000 Subject: gnu: r-shinydashboard: Update to 0.7.2. * gnu/packages/cran.scm (r-shinydashboard): Update to 0.7.2. [native-inputs]: Remove node-uglify-js; add esbuild. [arguments]: Remove modules; use esbuild in build phase 'generate-minified-javascript. --- gnu/packages/cran.scm | 23 +++++++++++------------ 1 file changed, 11 insertions(+), 12 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6ac81d7c6a..0d77936ebf 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2262,36 +2262,35 @@ supports interactive trees, to enable rich, editable trees in Shiny.") (define-public r-shinydashboard (package (name "r-shinydashboard") - (version "0.7.1") + (version "0.7.2") (source (origin (method url-fetch) (uri (cran-uri "shinydashboard" version)) (sha256 (base32 - "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i")))) + "0hrqkwlpb8rnmp5j74p134g4c4cl16icmwc2ip6k1634fa2y8vm5")))) (build-system r-build-system) ;; The directory inst/AdminLTE/ contains a minified JavaScript file. ;; Regenerate it from the included sources. (arguments - `(#:modules ((guix build utils) - (guix build r-build-system) - (ice-9 popen)) - #:phases + `(#:phases (modify-phases %standard-phases (add-after 'unpack 'generate-minified-javascript (lambda _ (with-directory-excursion "inst/AdminLTE" - (delete-file "app.min.js") - (let ((minified (open-pipe* OPEN_READ "uglifyjs" "app.js"))) - (call-with-output-file "app.min.js" - (lambda (port) - (dump-port minified port)))))))))) + (let ((target "app.min.js") + (source "app.js")) + (format #t "Processing ~a --> ~a~%" + source target) + (delete-file target) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target))))))))) (propagated-inputs `(("r-htmltools" ,r-htmltools) ("r-promises" ,r-promises) ("r-shiny" ,r-shiny))) (native-inputs - `(("uglifyjs" ,node-uglify-js))) + `(("esbuild" ,esbuild))) (home-page "https://rstudio.github.io/shinydashboard/") (synopsis "Create dashboards with shiny") (description "This package provides an extension to the Shiny web -- cgit 1.4.1 From d4ae183b6e3a33bb7fe86b00a964d5928c30cc69 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:15 +0000 Subject: gnu: r-geosphere: Update to 1.5-14. * gnu/packages/cran.scm (r-geosphere): Update to 1.5-14. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0d77936ebf..1c67b5ff19 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2796,14 +2796,14 @@ coordinates.") (define-public r-geosphere (package (name "r-geosphere") - (version "1.5-10") + (version "1.5-14") (source (origin (method url-fetch) (uri (cran-uri "geosphere" version)) (sha256 (base32 - "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan")))) + "0bg4vfmrw140j2ax0p6bflvb77w03ir39wa87l96rj473jpa9hzj")))) (build-system r-build-system) (propagated-inputs `(("r-sp" ,r-sp))) (home-page "https://cran.r-project.org/web/packages/geosphere") -- cgit 1.4.1 From ea5915097c06e5533756fd456f9d1c4a241106f7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:15 +0000 Subject: gnu: r-pkgload: Update to 1.2.3. * gnu/packages/cran.scm (r-pkgload): Update to 1.2.3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1c67b5ff19..2332082551 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3211,14 +3211,14 @@ is configured appropriately so R can use them.") (define-public r-pkgload (package (name "r-pkgload") - (version "1.2.2") + (version "1.2.3") (source (origin (method url-fetch) (uri (cran-uri "pkgload" version)) (sha256 (base32 - "0yxvik8kij0mqlki46hf6xnbfvmxwk0r2a3zwjpg0fwcd2s835a8")))) + "0jdkaj5cl0viy0i0hkcm4n2wlg1mfv3camr7f385njfararfanhh")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) -- cgit 1.4.1 From 77c794051689267c42ea7a0293ed9196b41ce5e4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:15 +0000 Subject: gnu: r-fitdistrplus: Update to 1.1-6. * gnu/packages/cran.scm (r-fitdistrplus): Update to 1.1-6. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2332082551..27b4ae0a97 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4247,14 +4247,14 @@ functions from LINPACK.") (define-public r-fitdistrplus (package (name "r-fitdistrplus") - (version "1.1-5") + (version "1.1-6") (source (origin (method url-fetch) (uri (cran-uri "fitdistrplus" version)) (sha256 (base32 - "1p9rvvh05zqb9vzhcyzdh7i8lbmb53nj8nyn0gqcmp7wafg9cd1f")))) + "1glnbcm1gghzgvzpxcfsmn7dp2f9jqyx39n3ydwp9fx38409khhp")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) -- cgit 1.4.1 From ecc16a884f576a326a3fd938a40a8a0333a8878a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:16 +0000 Subject: gnu: r-rpostgresql: Update to 0.7-3. * gnu/packages/cran.scm (r-rpostgresql): Update to 0.7-3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 27b4ae0a97..931c3f4275 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4609,14 +4609,14 @@ the RMariaDB package.") (define-public r-rpostgresql (package (name "r-rpostgresql") - (version "0.7") + (version "0.7-3") (source (origin (method url-fetch) (uri (cran-uri "RPostgreSQL" version)) (sha256 (base32 - "1bqfdbs09f65ssc6bx4z3kkmia8ja6qbnijxizw63p0fbcakq2q4")))) + "1fbixmnjp1kh6yiv8zhg8zi5ryvdf5j2jxv4agq5gcxf541s3g5x")))) (properties `((upstream-name . "RPostgreSQL"))) (build-system r-build-system) (inputs -- cgit 1.4.1 From 35e056d040febf8c31c59a98481396c4479b84d2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:16 +0000 Subject: gnu: r-recipes: Update to 0.1.17. * gnu/packages/cran.scm (r-recipes): Update to 0.1.17. [propagated-inputs]: Add r-vctrs. --- gnu/packages/cran.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 931c3f4275..b07aa39352 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4888,14 +4888,14 @@ provides a one-row summary of model-level statistics.") (define-public r-recipes (package (name "r-recipes") - (version "0.1.16") + (version "0.1.17") (source (origin (method url-fetch) (uri (cran-uri "recipes" version)) (sha256 (base32 - "1mayfdbn6q775d4gbdjrrhdbmpsxga57kwh0h7bwv8rk0vmvik23")))) + "0gbdc5kvbn14s5zrf4vrdjvkfajs00p7vvb433ii0lqnl07bl87d")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) @@ -4914,6 +4914,7 @@ provides a one-row summary of model-level statistics.") ("r-tidyr" ,r-tidyr) ("r-tidyselect" ,r-tidyselect) ("r-timedate" ,r-timedate) + ("r-vctrs" ,r-vctrs) ("r-withr" ,r-withr))) (native-inputs `(("r-knitr" ,r-knitr))) -- cgit 1.4.1 From 28c70629007eb80a1a3b6fac238f45325732847e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:16 +0000 Subject: gnu: r-mitml: Update to 0.4-3. * gnu/packages/cran.scm (r-mitml): Update to 0.4-3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b07aa39352..9a3b52fe13 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5159,14 +5159,14 @@ clustered data.") (define-public r-mitml (package (name "r-mitml") - (version "0.4-2") + (version "0.4-3") (source (origin (method url-fetch) (uri (cran-uri "mitml" version)) (sha256 (base32 - "0zrmchsk012linw3m5rda6hj8xpxpwzbf4alq0nc1pzvl99aa558")))) + "00i18nnvrdrg91crgcp2a431xs71cawaip3xkqk2myv0iav3xga9")))) (build-system r-build-system) (propagated-inputs `(("r-haven" ,r-haven) -- cgit 1.4.1 From d61b18187ebd7845e89b6899acba43d30df3e0ab Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:17 +0000 Subject: gnu: r-laeken: Update to 0.5.2. * gnu/packages/cran.scm (r-laeken): Update to 0.5.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9a3b52fe13..ae03565780 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5445,14 +5445,14 @@ where possible.") (define-public r-laeken (package (name "r-laeken") - (version "0.5.1") + (version "0.5.2") (source (origin (method url-fetch) (uri (cran-uri "laeken" version)) (sha256 (base32 - "199rjkhjjygpr6cjzab87as46acb5npi44m4yycvk7lnd0blma8s")))) + "1p3ccbaydlr52p8qmgmm2l6kryvq6jjjx7mqn2vv0gpjaxqhyy92")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) -- cgit 1.4.1 From ca7c2ff37333e0eef9a5f016c0488db9e16ae6cf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:17 +0000 Subject: gnu: r-vcd: Update to 1.4-9. * gnu/packages/cran.scm (r-vcd): Update to 1.4-9. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ae03565780..8b6dc6b3cb 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5467,14 +5467,14 @@ modeling for empirical income distributions.") (define-public r-vcd (package (name "r-vcd") - (version "1.4-8") + (version "1.4-9") (source (origin (method url-fetch) (uri (cran-uri "vcd" version)) (sha256 (base32 - "030yyhpzsj4ivwrla7p9kgvmyjh6b8fr7czf678ykxjj64ccnvr3")))) + "13sn77qdcyll9lz7nab0bxzfvpgj8f5rl2cq5ylpz8pibynj1d55")))) (build-system r-build-system) (propagated-inputs `(("r-colorspace" ,r-colorspace) -- cgit 1.4.1 From 8293cd4cce67506183e073f7c6eb7ba1e7cde9ae Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:17 +0000 Subject: gnu: r-tsp: Update to 1.1-11. * gnu/packages/cran.scm (r-tsp): Update to 1.1-11. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8b6dc6b3cb..049049cf3e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5753,14 +5753,14 @@ timeout. It can also poll several processes at once.") (define-public r-tsp (package (name "r-tsp") - (version "1.1-10") + (version "1.1-11") (source (origin (method url-fetch) (uri (cran-uri "TSP" version)) (sha256 (base32 - "0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4")))) + "0gdwxbj2gria7jhsswmfvc32r43sdd63z3lyy21gbvmfcakvb8j9")))) (properties `((upstream-name . "TSP"))) (build-system r-build-system) (propagated-inputs `(("r-foreach" ,r-foreach))) -- cgit 1.4.1 From 99e504adf7806a0c840e06093b97923baa0df803 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:17 +0000 Subject: gnu: r-seriation: Update to 1.3.1. * gnu/packages/cran.scm (r-seriation): Update to 1.3.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 049049cf3e..10a4fbf4c7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5840,14 +5840,14 @@ Markdown documents.") (define-public r-seriation (package (name "r-seriation") - (version "1.3.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "seriation" version)) (sha256 (base32 - "1vl0zfdvxdccvda8lwkjhg5rivj2q5gjm4qvkqwny6asm06x80ny")))) + "08c37n3xxc4n4vbkw38k3l3hdlmck8drqpl6z274vkgi2sqv8qyf")))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster) -- cgit 1.4.1 From a0c4b703055def8ddddbfc0afd656e307f781565 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:18 +0000 Subject: gnu: r-xfun: Update to 0.27. * gnu/packages/cran.scm (r-xfun): Update to 0.27. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 10a4fbf4c7..7ddaae7497 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5872,13 +5872,13 @@ iVAT).") (define-public r-xfun (package (name "r-xfun") - (version "0.26") + (version "0.27") (source (origin (method url-fetch) (uri (cran-uri "xfun" version)) (sha256 - (base32 "1997s00dzkyj15xk9w1r2h6i49srpgqzvhhyvd5pk1kwkd4809ly")))) + (base32 "11alh3kasiizfar0f667m5sj3s5443fggjv0541ghmxwlqrvyxf7")))) (build-system r-build-system) ;; knitr itself depends on xfun #; -- cgit 1.4.1 From 8c61a824183b4ca5a62bffcf1e9f25644e944583 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:18 +0000 Subject: gnu: r-pillar: Update to 1.6.4. * gnu/packages/cran.scm (r-pillar): Update to 1.6.4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7ddaae7497..08acbd340c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5976,14 +5976,14 @@ to variables on the left-hand side of the assignment.") (define-public r-pillar (package (name "r-pillar") - (version "1.6.3") + (version "1.6.4") (source (origin (method url-fetch) (uri (cran-uri "pillar" version)) (sha256 (base32 - "1ica4zjr3kmcpqh2668nmsv5dbvm4yri5952vcxja4djsgfnry3j")))) + "17m13rzgwdddwa0n3gpmax6wmfaphbg71l13ffhw5vnxf6i94fh3")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) -- cgit 1.4.1 From 28a337f9f4f7f2a222d59e160664018d48e8a73d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:18 +0000 Subject: gnu: r-tinytex: Update to 0.34. * gnu/packages/cran.scm (r-tinytex): Update to 0.34. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 08acbd340c..d86dbfc348 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6045,14 +6045,14 @@ packages that work with genomic data.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.33") + (version "0.34") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "10lqn704dqv5k5v6y964l8c77rwy4ilrc1hcb99j4vxpx3p4nd43")))) + "16z6v06pmvg02rbxkqyiidasg1dryy759zabnqjw6y85nybr618x")))) (build-system r-build-system) (propagated-inputs `(("r-xfun" ,r-xfun))) -- cgit 1.4.1 From a511e032deb64c1a39c98d051f5e2f1e970c01df Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:19 +0000 Subject: gnu: r-ifultools: Update to 2.0-23. * gnu/packages/cran.scm (r-ifultools): Update to 2.0-23. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d86dbfc348..95ccd02638 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6339,14 +6339,14 @@ provides some missing S-PLUS functionality in R.") (define-public r-ifultools (package (name "r-ifultools") - (version "2.0-22") + (version "2.0-23") (source (origin (method url-fetch) (uri (cran-uri "ifultools" version)) (sha256 (base32 - "0f95vqc47dgssqngznk0rclr72ndbyxc7gdq2cmbksvq7qpn3gg1")))) + "16a7rbvlym3bnfm93ikr5kl0l86ppk0s41fva6idvcx765g3fqkk")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) -- cgit 1.4.1 From 342ee971024042019734608ebd5fec1c37412d60 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:19 +0000 Subject: gnu: r-heatmaply: Update to 1.3.0. * gnu/packages/cran.scm (r-heatmaply): Update to 1.3.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 95ccd02638..f6b07044c6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6795,14 +6795,14 @@ powerful and convenient features.") (define-public r-heatmaply (package (name "r-heatmaply") - (version "1.2.1") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "heatmaply" version)) (sha256 (base32 - "0hspfkninwy62sf8gkdcsvwnvl66bbnjs2dpah9rr95a3rsgdp9d")))) + "1w8yyzb68laxd4zxycvgmpqj5wnyidjgv1vbzbxndp9p92f2cp8a")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) -- cgit 1.4.1 From e23c15280139a71e2407545044221a5f2fa6ea01 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:19 +0000 Subject: gnu: r-rastervis: Update to 0.51.0. * gnu/packages/cran.scm (r-rastervis): Update to 0.51.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f6b07044c6..af9882a790 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7919,14 +7919,14 @@ Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.") (define-public r-rastervis (package (name "r-rastervis") - (version "0.50.3") + (version "0.51.0") (source (origin (method url-fetch) (uri (cran-uri "rasterVis" version)) (sha256 (base32 - "10njks2kwyh5rp2b6sf2hffxzzwwhskb8m98l73p8yrvsdri1gyj")))) + "1gkn5na7cspnh3qpmi4k5n65crmp8c2s106g8hh51lsdvm5369aj")))) (properties `((upstream-name . "rasterVis"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From f9c40e0169a619d78e314b0fc1e6f8f643ed7358 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:19 +0000 Subject: gnu: r-rjags: Update to 4-12. * gnu/packages/cran.scm (r-rjags): Update to 4-12. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index af9882a790..13c5f1af59 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8548,14 +8548,14 @@ functions.") (define-public r-rjags (package (name "r-rjags") - (version "4-11") + (version "4-12") (source (origin (method url-fetch) (uri (cran-uri "rjags" version)) (sha256 (base32 - "0vs86jji4h26y8aczy8r08jiq7ax0idlrm87mmvaa5sxlqmqa705")))) + "041y4zfr50y96g0kl857jcba0a3gpdpk8qfn9fj8zxzbz71k87xr")))) (build-system r-build-system) (propagated-inputs `(("r-coda" ,r-coda))) -- cgit 1.4.1 From 2936dec5d874f58094b02b982bb6e7c9d368b5f2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:19 +0000 Subject: gnu: r-rbibutils: Update to 2.2.4. * gnu/packages/cran.scm (r-rbibutils): Update to 2.2.4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 13c5f1af59..380856d311 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8574,14 +8574,14 @@ hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.") (define-public r-rbibutils (package (name "r-rbibutils") - (version "2.2.3") + (version "2.2.4") (source (origin (method url-fetch) (uri (cran-uri "rbibutils" version)) (sha256 (base32 - "1rzc2icik26qlnrbq58c24lc9m0grl83p0hyr70whallqfipa174")))) + "15yyihk0dgz3yyqz28r5nc6m99zcywpabnabf18phbs7rb87p7mv")))) (properties `((upstream-name . "rbibutils"))) (build-system r-build-system) (home-page "https://geobosh.github.io/rbibutils/") -- cgit 1.4.1 From e0a7b783ea4344ae854c41f4a5642cdfabc9661b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:20 +0000 Subject: gnu: r-entropy: Update to 1.3.1. * gnu/packages/cran.scm (r-entropy): Update to 1.3.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 380856d311..c061f3cc82 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8708,14 +8708,14 @@ reduced-bias estimates.") (define-public r-entropy (package (name "r-entropy") - (version "1.3.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "entropy" version)) (sha256 (base32 - "0fhhsy8ci9c73xwr2b167dfix0b7kqsk6kf46qqv1lmvbv11vxqa")))) + "1f0j8jsn6pzf4gi5g0akixx6x5vc69ci5f4m2vnwp40frvsqjnkg")))) (properties `((upstream-name . "entropy"))) (build-system r-build-system) (home-page "https://www.strimmerlab.org/software/entropy/") -- cgit 1.4.1 From 110cf6dd463d3ed3ec03a4528bf5818e032c0fba Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:20 +0000 Subject: gnu: r-insight: Update to 0.14.5. * gnu/packages/cran.scm (r-insight): Update to 0.14.5. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c061f3cc82..6e2d78d349 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8848,14 +8848,14 @@ other add-on packages.") (define-public r-insight (package (name "r-insight") - (version "0.14.4") + (version "0.14.5") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 - "0h63nr337zbczbj9izyb7g5dlzwail5w70hbbn45paq6vybkqks3")))) + "10kc72g2hfsiipba4kalda1wxsb01nq2ax2yim386bkk0vjszwfx")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) -- cgit 1.4.1 From 99b1b197b8d0db80ae8ec8cb5c90afdaf8fc4474 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:20 +0000 Subject: gnu: r-flextable: Update to 0.6.9. * gnu/packages/cran.scm (r-flextable): Update to 0.6.9. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6e2d78d349..27a24e430f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8984,14 +8984,14 @@ functions.") (define-public r-flextable (package (name "r-flextable") - (version "0.6.8") + (version "0.6.9") (source (origin (method url-fetch) (uri (cran-uri "flextable" version)) (sha256 (base32 - "1b4hyrarxbk4d1ma5gy162b13nm5r5ysi049bxgcfim50rh40igs")))) + "15lba98wnci2nsndj86gx3k94q9lfxhp5nr5xlhgcnycyj1c9zjx")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) -- cgit 1.4.1 From 1dc2e808f3ddb28fb17b6c4a565f959f36b2d037 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:21 +0000 Subject: gnu: r-argparse: Update to 2.1.2. * gnu/packages/cran.scm (r-argparse): Update to 2.1.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 27a24e430f..e2c0c23bd7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9136,14 +9136,14 @@ matches version and feature constraints.") (define-public r-argparse (package (name "r-argparse") - (version "2.1.1") + (version "2.1.2") (source (origin (method url-fetch) (uri (cran-uri "argparse" version)) (sha256 (base32 - "1k6v35g3bppcr896h4v39zh1sxxia1bxxh29xv0mhad1nvmv25j9")))) + "1cz5qlxw3v8smd5vb00wlzy02mx5i0infm5hnq55hnakffd3b5wr")))) (build-system r-build-system) (inputs `(("python" ,python))) (propagated-inputs -- cgit 1.4.1 From 942bb482f132667cd19bfc2d3f1783ec685ace0c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:21 +0000 Subject: gnu: r-rootsolve: Update to 1.8.2.3. * gnu/packages/cran.scm (r-rootsolve): Update to 1.8.2.3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e2c0c23bd7..e88e547598 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9369,14 +9369,14 @@ bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.") (define-public r-rootsolve (package (name "r-rootsolve") - (version "1.8.2.2") + (version "1.8.2.3") (source (origin (method url-fetch) (uri (cran-uri "rootSolve" version)) (sha256 (base32 - "1p7nh09g2815vqpvi6c5vvjshkwjn00nx5d3gdyjs304q5312q0a")))) + "182bb727sgqi5f3pzmw8jnn328wdjrgj9lfvg49gv8s22rjd3cxm")))) (properties `((upstream-name . "rootSolve"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) -- cgit 1.4.1 From 8727af3b2ee02fff54858b3cc3e4abbb09247602 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:21 +0000 Subject: gnu: r-manipulatewidget: Update to 0.11.1. * gnu/packages/cran.scm (r-manipulatewidget): Update to 0.11.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e88e547598..114e6d1d3c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9445,13 +9445,13 @@ based on index arrays and simple triplet representations, respectively.") (define-public r-manipulatewidget (package (name "r-manipulatewidget") - (version "0.11.0") + (version "0.11.1") (source (origin (method url-fetch) (uri (cran-uri "manipulateWidget" version)) (sha256 - (base32 "0iysgl6ab8fvg1xxdx6hr3swqwbkfqzjkk4x5sbvmawbl2a395gj")))) + (base32 "1dpgzmiv08afm57yxr017b014lfn9h3pa4w65prk5k3dgn6p4wsv")))) (properties `((upstream-name . "manipulateWidget"))) (build-system r-build-system) -- cgit 1.4.1 From 76185fdae231cec433280ca29de61232a8d2272c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:22 +0000 Subject: gnu: r-cmplot: Update to 3.7.0. * gnu/packages/cran.scm (r-cmplot): Update to 3.7.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 114e6d1d3c..843b88cd5e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9548,14 +9548,14 @@ from the @code{stats} package (plus some extra parameters).") (define-public r-cmplot (package (name "r-cmplot") - (version "3.6.2") + (version "3.7.0") (source (origin (method url-fetch) (uri (cran-uri "CMplot" version)) (sha256 (base32 - "13y05j5gsdc712fn7yvcz5nx2pbcdvl201hfb6jzpvl86qx2l0j1")))) + "0d6ww8pdrawdg5acbhiyi2jpmapf2ghixy9mi4kmsq8yg36pksfh")))) (properties `((upstream-name . "CMplot"))) (build-system r-build-system) (home-page "https://github.com/YinLiLin/CMplot") -- cgit 1.4.1 From de43669e60cb01dc4137c7c675189609dfd4f1d3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:22 +0000 Subject: gnu: r-qualv: Update to 0.3-4. * gnu/packages/cran.scm (r-qualv): Update to 0.3-4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 843b88cd5e..c47409d889 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9980,14 +9980,14 @@ data with multiple data types.") (define-public r-qualv (package (name "r-qualv") - (version "0.3-3") + (version "0.3-4") (source (origin (method url-fetch) (uri (cran-uri "qualV" version)) (sha256 (base32 - "1yyqk223ydcc0125gsn33a4mcdp8bd76fpn8kj9bfz9g78b8dqmx")))) + "0rkjzva2h158d5c631jmjjh7qjibbyisl0503san80rk9fgxl45b")))) (properties `((upstream-name . "qualV"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From cf4d90becc5d1770ac775afe56ef0b1a732114c8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:22 +0000 Subject: gnu: r-raster: Update to 3.5-2. * gnu/packages/cran.scm (r-raster): Update to 3.5-2. [propagated-inputs]: Add r-terra. --- gnu/packages/cran.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c47409d889..1c7a2f37a6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10120,18 +10120,19 @@ used to teach mathematics, statistics, computation and modeling.") (define-public r-raster (package (name "r-raster") - (version "3.4-13") + (version "3.5-2") (source (origin (method url-fetch) (uri (cran-uri "raster" version)) (sha256 (base32 - "120k4bkgwddrx8ijgdhsgjz8g8dxcwp9bx3kfzrhw00q1b289hir")))) + "0wixw1ixnmcmkwczpj8m90c76727zira2rl4ighashggydkm2mlr")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) - ("r-sp" ,r-sp))) + ("r-sp" ,r-sp) + ("r-terra" ,r-terra))) (home-page "https://www.rspatial.org/") (synopsis "Geographic data analysis and modeling") (description -- cgit 1.4.1 From aa0d27b4e2b998b808e70d2886d7c3eb26159609 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:23 +0000 Subject: gnu: r-acceptancesampling: Update to 1.0-7. * gnu/packages/cran.scm (r-acceptancesampling): Update to 1.0-7. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1c7a2f37a6..3bfec5bbd0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11013,13 +11013,13 @@ series.") (define-public r-acceptancesampling (package (name "r-acceptancesampling") - (version "1.0-6") + (version "1.0-7") (source (origin (method url-fetch) (uri (cran-uri "AcceptanceSampling" version)) (sha256 - (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9")))) + (base32 "13k3zczjycw24n5yp0qmrm233id5j8h6fvra57f1n6js7ljxiiq2")))) (properties `((upstream-name . "AcceptanceSampling"))) (build-system r-build-system) -- cgit 1.4.1 From e1469d55f0f7f26b06929c850596d14858b4f855 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:23 +0000 Subject: gnu: r-th-data: Update to 1.1-0. * gnu/packages/cran.scm (r-th-data): Update to 1.1-0. [native-inputs]: Add r-knitr. --- gnu/packages/cran.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3bfec5bbd0..583a5608dd 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11111,19 +11111,21 @@ cross-sectional, time series, clustered, panel, and longitudinal data.") (define-public r-th-data (package (name "r-th-data") - (version "1.0-10") + (version "1.1-0") (source (origin (method url-fetch) (uri (cran-uri "TH.data" version)) (sha256 (base32 - "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1")))) + "0ghihfpk5d8gsdlzf6phw7dwwz3adx64pxk82vlmlqx53ljpxcr1")))) (properties `((upstream-name . "TH.data"))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) ("r-survival" ,r-survival))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/TH.data/") (synopsis "Shared data sets") (description -- cgit 1.4.1 From ba77d9096a11b0e2a119951cf6885236da8e421b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:23 +0000 Subject: gnu: r-emmeans: Update to 1.7.0. * gnu/packages/cran.scm (r-emmeans): Update to 1.7.0. [propagated-inputs]: Remove r-plyr. --- gnu/packages/cran.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 583a5608dd..50167bb562 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11164,20 +11164,19 @@ Hothorn, Westfall, 2010, CRC Press).") (define-public r-emmeans (package (name "r-emmeans") - (version "1.6.3") + (version "1.7.0") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "1mwcq3hvpx04qnn5k0bv1mikjgm9mk6m83i8hj350s1c1a0mi40n")))) + "1ig94mjifhhygznv2xv1gl8hdvk618w5fcmkaj1xmpwpc64m9dnl")))) (build-system r-build-system) (propagated-inputs `(("r-estimability" ,r-estimability) ("r-mvtnorm" ,r-mvtnorm) ("r-numderiv" ,r-numderiv) - ("r-plyr" ,r-plyr) ("r-xtable" ,r-xtable))) (native-inputs `(("r-knitr" ,r-knitr))) -- cgit 1.4.1 From 8492e24a1fd557d9118dcddae3c6337fcb12d663 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:24 +0000 Subject: gnu: r-libcoin: Update to 1.0-9. * gnu/packages/cran.scm (r-libcoin): Update to 1.0-9. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 50167bb562..d8c4c54f0a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11214,13 +11214,13 @@ Cohen (1988).") (define-public r-libcoin (package (name "r-libcoin") - (version "1.0-8") + (version "1.0-9") (source (origin (method url-fetch) (uri (cran-uri "libcoin" version)) (sha256 - (base32 "0izgnr4zdrbz3a05b0s28xfly4izp2zslgh282l9ads4skrmj3hl")))) + (base32 "1syrcdj5qg5m3zd3dlxgpfklswbalfg42w058dr09hnzqsvx0z9d")))) (build-system r-build-system) (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm))) (home-page "https://cran.r-project.org/web/packages/libcoin") -- cgit 1.4.1 From bc26a9db39889b7fb423884e2ecde57f29b3aa6c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:24 +0000 Subject: gnu: r-coin: Update to 1.4-2. * gnu/packages/cran.scm (r-coin): Update to 1.4-2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d8c4c54f0a..2a08cf5543 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11233,14 +11233,14 @@ and permutation inference in the framework of Strasser and Weber (1999).") (define-public r-coin (package (name "r-coin") - (version "1.4-1") + (version "1.4-2") (source (origin (method url-fetch) (uri (cran-uri "coin" version)) (sha256 (base32 - "15xvhnbyg34aacn6jfz4bsa1f7wq2ci0hslj8mgymql90k50x1qi")))) + "1cpv7jx840inzg98bkhrb5yscx0gpag6br237r5qpnc2gbrd2ikm")))) (build-system r-build-system) (propagated-inputs `(("r-libcoin" ,r-libcoin) -- cgit 1.4.1 From 4b20190e11af6d805880f88725ac77e7a3857544 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:24 +0000 Subject: gnu: r-tmb: Update to 1.7.22. * gnu/packages/cran.scm (r-tmb): Update to 1.7.22. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2a08cf5543..33c92ef31c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11295,14 +11295,14 @@ Bayesian modeling.") (define-public r-tmb (package (name "r-tmb") - (version "1.7.21") + (version "1.7.22") (source (origin (method url-fetch) (uri (cran-uri "TMB" version)) (sha256 (base32 - "1lf9vf28l48xhw2irxfxl4vsqzj7skzblydw32p18zddzpapl0z9")))) + "116k7ffgadhkqq4lckfd4403qvybcls1hcs1ap1b7lkylghjahf2")))) (properties `((upstream-name . "TMB"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 250e8858411d709c5eaced5cc8de41abad65d180 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:24 +0000 Subject: gnu: r-performance: Update to 0.8.0. * gnu/packages/cran.scm (r-performance): Update to 0.8.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 33c92ef31c..0f39fc8e4b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11427,14 +11427,14 @@ ROPE percentage and pd).") (define-public r-performance (package (name "r-performance") - (version "0.7.3") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "performance" version)) (sha256 (base32 - "03qdsdl4x3hwqlbs7hlqb73xypd13p5zj519y0zcydqkf25391sp")))) + "1xjjnhqmwfflm5yfgjhycjn0fj0manvsvkk2ppifn0373bajp5n2")))) (build-system r-build-system) (propagated-inputs `(("r-bayestestr" ,r-bayestestr) -- cgit 1.4.1 From 2ecee21fe8c44e51199112e1d2a7c002b16ffbd7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:25 +0000 Subject: gnu: r-effectsize: Update to 0.5. * gnu/packages/cran.scm (r-effectsize): Update to 0.5. [propagated-inputs]: Add r-datawizard and r-performance. --- gnu/packages/cran.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0f39fc8e4b..7ee4c8874a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11485,20 +11485,22 @@ results using @code{ggplot2}.") (define-public r-effectsize (package (name "r-effectsize") - (version "0.4.5") + (version "0.5") (source (origin (method url-fetch) (uri (cran-uri "effectsize" version)) (sha256 (base32 - "0rp0r75p8q467lmrsr1gl9wjpib9jz7ksx5rm6c7q2lfg9b9zrjf")))) + "0w7m3hzmwral9cycpvknrkbdvgk230b3vg5sxbm84x72mw534hnh")))) (properties `((upstream-name . "effectsize"))) (build-system r-build-system) (propagated-inputs `(("r-bayestestr" ,r-bayestestr) + ("r-datawizard" ,r-datawizard) ("r-insight" ,r-insight) - ("r-parameters" ,r-parameters))) + ("r-parameters" ,r-parameters) + ("r-performance" ,r-performance))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/easystats/effectsize") -- cgit 1.4.1 From 212ee4240a7ca43eb22919cc7a4c34d734db58ea Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:25 +0000 Subject: gnu: r-usethis: Update to 2.1.0. * gnu/packages/cran.scm (r-usethis): Update to 2.1.0. [propagated-inputs]: Add r-ellipsis. --- gnu/packages/cran.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7ee4c8874a..b231d4b9e9 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11752,14 +11752,14 @@ User credentials are shared with command line git through the (define-public r-usethis (package (name "r-usethis") - (version "2.0.1") + (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "usethis" version)) (sha256 (base32 - "1j6nzzrm2m6vi1gq0d5kxnnr9d8cy88wpmgigz3inych65x9w9pg")))) + "1s40rbr2z9bilsldp8pv5abrr7n0ixyxi2qqbf4hfhs14rhigncy")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) @@ -11767,6 +11767,7 @@ User credentials are shared with command line git through the ("r-crayon" ,r-crayon) ("r-curl" ,r-curl) ("r-desc" ,r-desc) + ("r-ellipsis" ,r-ellipsis) ("r-fs" ,r-fs) ("r-gert" ,r-gert) ("r-gh" ,r-gh) -- cgit 1.4.1 From 6813c6c1506b33bd1602e6e951f332d4d714e759 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:25 +0000 Subject: gnu: r-remotes: Update to 2.4.1. * gnu/packages/cran.scm (r-remotes): Update to 2.4.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b231d4b9e9..d466d3788d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11817,14 +11817,14 @@ more information about packages, and where they were installed from.") (define-public r-remotes (package (name "r-remotes") - (version "2.4.0") + (version "2.4.1") (source (origin (method url-fetch) (uri (cran-uri "remotes" version)) (sha256 (base32 - "048lihmwksl72fg4fdmhihblj9ipxl22x9wfpgwsbsv79zjc7rfd")))) + "0xij8x4ga0r7rp2lxx9hw1zlzv48mfg56v8nf03gsw0dw6r7gmym")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) -- cgit 1.4.1 From 64b3d356bb568fab975ff88d8cec218cf33e720b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:26 +0000 Subject: gnu: r-rcmdcheck: Update to 1.4.0. * gnu/packages/cran.scm (r-rcmdcheck): Update to 1.4.0. [propagated-inputs]: Remove r-crayon; add r-curl. --- gnu/packages/cran.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d466d3788d..4d4ff8d00d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11861,19 +11861,19 @@ directories or URLs with their associated programs.") (define-public r-rcmdcheck (package (name "r-rcmdcheck") - (version "1.3.3") + (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "rcmdcheck" version)) (sha256 (base32 - "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs")))) + "1l696byn3kjq2xvz4wxybzaj6ink85h4lz3a35v2132ba5yyzm5v")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) ("r-cli" ,r-cli) - ("r-crayon" ,r-crayon) + ("r-curl" ,r-curl) ("r-desc" ,r-desc) ("r-digest" ,r-digest) ("r-pkgbuild" ,r-pkgbuild) -- cgit 1.4.1 From 581111b5b8b468537ed03304622004f400d510fe Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:26 +0000 Subject: gnu: r-rcppgsl: Update to 0.3.10. * gnu/packages/cran.scm (r-rcppgsl): Update to 0.3.10. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4d4ff8d00d..fafaf22bb2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -12070,13 +12070,13 @@ and related methods.") (define-public r-rcppgsl (package (name "r-rcppgsl") - (version "0.3.9") + (version "0.3.10") (source (origin (method url-fetch) (uri (cran-uri "RcppGSL" version)) (sha256 - (base32 "0zhfkn3w5q2k2ggizrikz9an8hm90g6mr60paq0z8xgp5hpkrlk6")))) + (base32 "0lalz51q31qqy0cr227vc3msi0h47p111lzy4zs93drgl1yhh4l6")))) (properties `((upstream-name . "RcppGSL"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 2d372617070578e61b9052752728492f5e384e9b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:26 +0000 Subject: gnu: r-misc3d: Update to 0.9-1. * gnu/packages/cran.scm (r-misc3d): Update to 0.9-1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index fafaf22bb2..26ca7f416a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -12501,14 +12501,14 @@ to colexicographical order.") (define-public r-misc3d (package (name "r-misc3d") - (version "0.9-0") + (version "0.9-1") (source (origin (method url-fetch) (uri (cran-uri "misc3d" version)) (sha256 (base32 - "10jf5r1x588vi54bzaqgi9mgcqlkiga2c3jvmqmk3lavc8fjksd1")))) + "0r9x57s63kx9f6dgam2nhbziq8nrs9wd8pk7g76hds2kw46vnyx0")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/misc3d/") (synopsis "Miscellaneous 3D Plots") -- cgit 1.4.1 From 81be1e2945f9e71d309c8c37b19aaae9af1de183 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:27 +0000 Subject: gnu: r-arm: Update to 1.12-2. * gnu/packages/cran.scm (r-arm): Update to 1.12-2. [propagated-inputs]: Remove r-hmisc. --- gnu/packages/cran.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 26ca7f416a..7d6afbae2e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -12580,19 +12580,18 @@ features (e.g. local modes).") (define-public r-arm (package (name "r-arm") - (version "1.11-2") + (version "1.12-2") (source (origin (method url-fetch) (uri (cran-uri "arm" version)) (sha256 (base32 - "1grb27vayr2vhyalzfqbhx6p278r7c3l4pzi5nrz3dmnyqrbx1c3")))) + "0pagrc1vkaz460d0lvrgb4xj6gcd920f4mrc8zpzw07c3v1s2sw1")))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) ("r-coda" ,r-coda) - ("r-hmisc" ,r-hmisc) ("r-lme4" ,r-lme4) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) -- cgit 1.4.1 From d15d9e350c12797192e4480b788abff49fc67a04 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:27 +0000 Subject: gnu: r-sodium: Update to 1.2.0. * gnu/packages/cran.scm (r-sodium): Update to 1.2.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7d6afbae2e..6e25dcb8e8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -12762,14 +12762,14 @@ Anderson-Darling Distribution\".") (define-public r-sodium (package (name "r-sodium") - (version "1.1") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "sodium" version)) (sha256 (base32 - "1zxzi8xvxnhgcd5qrylf08nz1cdq3aslrswjas440qg63ypmbf6w")))) + "0x4jb3cf1nv1spz1jc9xp8hly2b4a7nj48xr4s33jnfcpdjkmn5q")))) (properties `((upstream-name . "sodium"))) (build-system r-build-system) (inputs -- cgit 1.4.1 From a650d1a28aa6d1e1be6a73fb33f109153904275f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:27 +0000 Subject: gnu: r-rvcheck: Update to 0.2.1. * gnu/packages/cran.scm (r-rvcheck): Update to 0.2.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6e25dcb8e8..c91050ff97 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -13018,13 +13018,13 @@ manipulate tree data.") (define-public r-rvcheck (package (name "r-rvcheck") - (version "0.2.0") + (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "rvcheck" version)) (sha256 - (base32 "09gx29q882vh4q1qbb8z8lc3pgmpn7bk8skzcm85mrf3x3vgvkpa")))) + (base32 "09khjklvzbafd7r55496by01a9g3y291d87hpy43w44dmz9fzn9a")))) (build-system r-build-system) (propagated-inputs `(("r-biocmanager" ,r-biocmanager) -- cgit 1.4.1 From 19a0015f1cab8f8551b3b6cb23ce8047c9580a91 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:27 +0000 Subject: gnu: r-ore: Update to 1.7.0. * gnu/packages/cran.scm (r-ore): Update to 1.7.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c91050ff97..48f2a98570 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -13505,13 +13505,13 @@ creating color scales and calculating color distances.") (define-public r-ore (package (name "r-ore") - (version "1.6.3") + (version "1.7.0") (source (origin (method url-fetch) (uri (cran-uri "ore" version)) (sha256 - (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv")))) + (base32 "0qhbv7bynisr0prv7h0yxsxff7qdxfqza7i06xi4vn360kxx6w9g")))) (build-system r-build-system) (home-page "https://github.com/jonclayden/ore") (synopsis "R interface to the Onigmo regular expression library") -- cgit 1.4.1 From 9155a17351241f0fa4802287cfd20b350a39b33f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:28 +0000 Subject: gnu: r-grimport: Update to 0.9-4. * gnu/packages/cran.scm (r-grimport): Update to 0.9-4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 48f2a98570..914a6938af 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -13576,14 +13576,14 @@ handling.") (define-public r-grimport (package (name "r-grimport") - (version "0.9-3") + (version "0.9-4") (source (origin (method url-fetch) (uri (cran-uri "grImport" version)) (sha256 (base32 - "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd")))) + "0y9lsvfp1350das5v5d5pkv10z0n1crc7k4zn9inr94f9s4kjjr5")))) (properties `((upstream-name . "grImport"))) (build-system r-build-system) (inputs -- cgit 1.4.1 From 545a2f78a54579e6263b9199162f32e436f51415 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 17:52:28 +0000 Subject: gnu: r-rmpfr: Update to 0.8-5. * gnu/packages/cran.scm (r-rmpfr): Update to 0.8-5. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 914a6938af..a554c7e9f0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -13938,14 +13938,14 @@ limitations\" using the GNU Multiple Precision library.") (define-public r-rmpfr (package (name "r-rmpfr") - (version "0.8-4") + (version "0.8-5") (source (origin (method url-fetch) (uri (cran-uri "Rmpfr" version)) (sha256 (base32 - "0xaqbgkpnjg53zcp56c59cz5dh3jvvwqnzvyxqzy77c6yvkwy3hx")))) + "1a37zaahcyccb5kgad98z4dh9n75vffmiziv4al8axvihxqs5hjn")))) (properties `((upstream-name . "Rmpfr"))) (build-system r-build-system) (inputs -- cgit 1.4.1 From 2f61f562bb1bfc5772bdc0f878094fa7129d580a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:41:17 +0000 Subject: gnu: r-colourpicker: Update to 1.1.1. * gnu/packages/cran.scm (r-colourpicker): Update to 1.1.1. [arguments]: Remove modules; use esbuild in build phase 'process-javascript. [native-inputs]: Remove r-knitr and uglifyjs; add esbuild; change js-jquery version. --- gnu/packages/cran.scm | 46 ++++++++++++++++++---------------------------- 1 file changed, 18 insertions(+), 28 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a554c7e9f0..4cad5ece00 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15497,45 +15497,36 @@ to easily call your own custom JavaScript functions from R.") (define-public r-colourpicker (package (name "r-colourpicker") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "colourpicker" version)) (sha256 (base32 - "1qjispj7i12m02js5cm5xlgn5lyff0kc5ybz6lbknz8q5lkbdyrd")))) + "1q1wi3g403fbzp4ys3gsjbwdc86x770cx323qgi47ca8n219kl50")))) (build-system r-build-system) (arguments - `(#:modules ((guix build utils) - (guix build r-build-system) - (srfi srfi-1) - (ice-9 popen)) - #:phases + `(#:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst" - (call-with-values - (lambda () - (unzip2 + (let ((mapping `((,(assoc-ref inputs "js-salvattore") - "examples/colourInput/www/salvattore.min.js") + . "examples/colourInput/www/salvattore.min.js") (,(assoc-ref inputs "js-jquery") - "htmlwidgets/lib/jquery/jquery.min.js") + . "htmlwidgets/lib/jquery/jquery.min.js") ("www/shared/colourpicker/js/colourpicker.js" - "www/shared/colourpicker/js/colourpicker.min.js")))) - (lambda (sources targets) - (for-each (lambda (source target) - (format #t "Processing ~a --> ~a~%" - source target) - (delete-file target) - (let ((minified (open-pipe* OPEN_READ "uglifyjs" source))) - (call-with-output-file target - (lambda (port) - (dump-port minified port))))) - sources targets)))) - #t))))) + . "www/shared/colourpicker/js/colourpicker.min.js")))) + (for-each (lambda (source target) + (format #true "Processing ~a --> ~a~%" + source target) + (delete-file target) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target))) + (map car mapping) + (map cdr mapping))))))))) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-htmltools" ,r-htmltools) @@ -15545,15 +15536,14 @@ to easily call your own custom JavaScript functions from R.") ("r-shiny" ,r-shiny) ("r-shinyjs" ,r-shinyjs))) (native-inputs - `(("r-knitr" ,r-knitr) - ("uglifyjs" ,node-uglify-js) + `(("esbuild" ,esbuild) ("js-jquery" ,(origin (method url-fetch) - (uri "https://code.jquery.com/jquery-3.3.1.js") + (uri "https://code.jquery.com/jquery-1.11.3.js") (sha256 (base32 - "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq")))) + "1v956yf5spw0156rni5z77hzqwmby7ajwdcd6mkhb6zvl36awr90")))) ("js-salvattore" ,(origin (method url-fetch) -- cgit 1.4.1 From 4a6cfd218dc0a56fca8cca86ab95bc33d241a1b2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:40 +0000 Subject: gnu: r-sets: Update to 1.0-19. * gnu/packages/cran.scm (r-sets): Update to 1.0-19. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4cad5ece00..4ef564a0eb 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16200,14 +16200,14 @@ additional utilities for genomic regions processing.") (define-public r-sets (package (name "r-sets") - (version "1.0-18") + (version "1.0-19") (source (origin (method url-fetch) (uri (cran-uri "sets" version)) (sha256 (base32 - "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl")))) + "18185rm458nlifzrp73fjrjvksmm5dvn5ygs949kdzdln1myb4xf")))) (properties `((upstream-name . "sets"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/sets") -- cgit 1.4.1 From d0640880c4b3323a7f0a70d85cb63f06d6331db4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:41 +0000 Subject: gnu: r-spdata: Update to 2.0.1. * gnu/packages/cran.scm (r-spdata): Update to 2.0.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4ef564a0eb..6ee62a86c7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16462,14 +16462,14 @@ univariate class intervals for mapping or other graphics purposes.") (define-public r-spdata (package (name "r-spdata") - (version "0.3.10") + (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "spData" version)) (sha256 (base32 - "0c3kg2daz65znnmcaf5l108c88anzlfrsjlnmv2kxqr1lx8z9zl5")))) + "1z4hp5ivwzyvl8mkp98j2ng1cl1xksqbjxv85vdlqfqjwpia6df6")))) (properties `((upstream-name . "spData"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From e5256cfee7c5d876e5244d95ce5d86f4a34a5023 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:41 +0000 Subject: gnu: r-deldir: Update to 1.0-6. * gnu/packages/cran.scm (r-deldir): Update to 1.0-6. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6ee62a86c7..034dd8f532 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16515,14 +16515,14 @@ sampling.") (define-public r-deldir (package (name "r-deldir") - (version "0.2-10") + (version "1.0-6") (source (origin (method url-fetch) (uri (cran-uri "deldir" version)) (sha256 (base32 - "08ij6zb6id71zk6gzs9z779y49y41c2gpi7p7mljnlw7py92g8k5")))) + "1igq0l2knsbhizncgydcsidgkvvlwwlkrifbcdyhnzk0bhrdixkd")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/deldir") -- cgit 1.4.1 From c93f24136879a3c6bb49aab43fed31ba29ad0774 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:41 +0000 Subject: gnu: r-s2: Update to 1.0.7. * gnu/packages/cran.scm (r-s2): Update to 1.0.7. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 034dd8f532..816de7c4cc 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16565,14 +16565,14 @@ high-performance functions are provided here.") (define-public r-s2 (package (name "r-s2") - (version "1.0.6") + (version "1.0.7") (source (origin (method url-fetch) (uri (cran-uri "s2" version)) (sha256 (base32 - "1xd42bpbm090dqlldavbn6c1h1mfwhlws9536avan00w3szlxk56")))) + "0gwydn6wdl675ydkcckrci6ylcx30qn8nfhmrp4qx4r9mv3c2410")))) (properties `((upstream-name . "s2"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 545f0c9cd1bd1a7e3cb66053c8470eafb0167717 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:41 +0000 Subject: gnu: r-sf: Update to 1.0-3. * gnu/packages/cran.scm (r-sf): Update to 1.0-3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 816de7c4cc..5bc98193e1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16596,14 +16596,14 @@ information about geometries.") (define-public r-sf (package (name "r-sf") - (version "1.0-2") + (version "1.0-3") (source (origin (method url-fetch) (uri (cran-uri "sf" version)) (sha256 (base32 - "0hh54krf4gjwrzxj2r3p5q7amdf8kblv8nm7hmbwmfv1rs30i1gc")))) + "1y1im0wxqx0vqas6ggmi6p1dyp98l895jy3asxky4vq5wpjfrqrf")))) (build-system r-build-system) (inputs `(("gdal" ,gdal) -- cgit 1.4.1 From ceb23d9fda6f1c88cf8ecb6c20fde62e07243d9b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:42 +0000 Subject: gnu: r-adegenet: Update to 2.1.5. * gnu/packages/cran.scm (r-adegenet): Update to 2.1.5. [propagated-inputs]: Remove r-spdep. --- gnu/packages/cran.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5bc98193e1..096b7cb43b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16686,14 +16686,14 @@ spanning tree.") (define-public r-adegenet (package (name "r-adegenet") - (version "2.1.4") + (version "2.1.5") (source (origin (method url-fetch) (uri (cran-uri "adegenet" version)) (sha256 (base32 - "0sxbw5l92xmkazndxbqaa2cxmgk8bqzzbk77q9li850s2i1fdssp")))) + "1wjp31634n6z6wglf4z3ydrhhn5jmpwwckmp3n2b0v5f3p2fivp4")))) (build-system r-build-system) (propagated-inputs `(("r-ade4" ,r-ade4) @@ -16706,7 +16706,6 @@ spanning tree.") ("r-reshape2" ,r-reshape2) ("r-seqinr" ,r-seqinr) ("r-shiny" ,r-shiny) - ("r-spdep" ,r-spdep) ("r-vegan" ,r-vegan))) (home-page "https://github.com/thibautjombart/adegenet") (synopsis "Exploratory analysis of genetic and genomic data") -- cgit 1.4.1 From 4df33663d4b87520158b76bc4758f6df2d35e8a1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:42 +0000 Subject: gnu: r-optparse: Update to 1.7.1. * gnu/packages/cran.scm (r-optparse): Update to 1.7.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 096b7cb43b..5a17ded38e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17134,14 +17134,14 @@ authoring books and technical documents with R Markdown.") (define-public r-optparse (package (name "r-optparse") - (version "1.6.6") + (version "1.7.1") (source (origin (method url-fetch) (uri (cran-uri "optparse" version)) (sha256 (base32 - "1l301dy3gc8pn7j00awcjh41wmc1ks9kswak255kbsa6f54rsxsi")))) + "1rqz0y4r94y3mwbb9kyz97cjqpnprka96qbncvbnbmgg2d630kij")))) (build-system r-build-system) (propagated-inputs `(("r-getopt" ,r-getopt))) -- cgit 1.4.1 From 2bad8896d9c2bd0f4d3d80a175e6ca863f45dddd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:42 +0000 Subject: gnu: r-svmisc: Update to 1.2.3. * gnu/packages/cran.scm (r-svmisc): Update to 1.2.3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5a17ded38e..311d5e106b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17323,14 +17323,14 @@ and accessing fields.") (define-public r-svmisc (package (name "r-svmisc") - (version "1.1.4") + (version "1.2.3") (source (origin (method url-fetch) (uri (cran-uri "svMisc" version)) (sha256 (base32 - "0y8mhiblyzwads4gf4whmxi7c6wdmqs3ahbj132l79bbdk40p83a")))) + "1r3kih5bnr4plnzdn5f2gg3xl3krgyl7gkdlf58a2l8vk13j3m9d")))) (properties `((upstream-name . "svMisc"))) (build-system r-build-system) (native-inputs -- cgit 1.4.1 From 0daba2ee2f550b1ae94d95abacfa540d64aa3a60 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:42 +0000 Subject: gnu: r-yulab-utils: Update to 0.0.4. * gnu/packages/cran.scm (r-yulab-utils): Update to 0.0.4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 311d5e106b..59b0ce0030 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17583,14 +17583,14 @@ package.") (define-public r-yulab-utils (package (name "r-yulab-utils") - (version "0.0.2") + (version "0.0.4") (source (origin (method url-fetch) (uri (cran-uri "yulab.utils" version)) (sha256 (base32 - "1haq6k0r64gs76p2vvrm42m64r8s32kzyz573pw9789y32zn0s5q")))) + "1bj93gnj7j4b7dgkbr5v22rsbwfcw5dvipl5irmidaakvrihd19q")))) (properties `((upstream-name . "yulab.utils"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=yulab.utils") -- cgit 1.4.1 From 65e36bcc9ad0fc1b0c175664817d006bd28f5828 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:43 +0000 Subject: gnu: r-pmcmr: Update to 4.4. * gnu/packages/cran.scm (r-pmcmr): Update to 4.4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 59b0ce0030..2d25133a83 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18408,14 +18408,14 @@ more generic data visualisation.") (define-public r-pmcmr (package (name "r-pmcmr") - (version "4.3") + (version "4.4") (source (origin (method url-fetch) (uri (cran-uri "PMCMR" version)) (sha256 (base32 - "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij")))) + "05n13pp5yff6pzk4ry07crddfaj3jlglrd1vkcnacyd8jpaxkd77")))) (properties `((upstream-name . "PMCMR"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/PMCMR/") -- cgit 1.4.1 From 56c52b9505f5c84a77d47f8b3f064465f1df5cb7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:43 +0000 Subject: gnu: r-mcmcpack: Update to 1.6-0. * gnu/packages/cran.scm (r-mcmcpack): Update to 1.6-0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2d25133a83..54dfc56ee2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18713,14 +18713,14 @@ multicore machines.") (define-public r-mcmcpack (package (name "r-mcmcpack") - (version "1.5-0") + (version "1.6-0") (source (origin (method url-fetch) (uri (cran-uri "MCMCpack" version)) (sha256 (base32 - "1khavqsimiwbfq7gyw5jyj67jxfd579pnc7mngnd655zc8yzspvr")))) + "16zjx8yz29ii75wfxj3p562l657bng8jnwzp2b54s7fiaws4kfdm")))) (properties `((upstream-name . "MCMCpack"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 89618cb5f498e9b1adc74fd811a2ca6bd96be313 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:43 +0000 Subject: gnu: r-clue: Update to 0.3-60. * gnu/packages/cran.scm (r-clue): Update to 0.3-60. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 54dfc56ee2..f7b76be239 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18999,14 +18999,14 @@ experiments in a well-organized and reproducible way.") (define-public r-clue (package (name "r-clue") - (version "0.3-59") + (version "0.3-60") (source (origin (method url-fetch) (uri (cran-uri "clue" version)) (sha256 (base32 - "0ychvjbqkcgqdp5gy4hsi4297phywd7fj89y3yi5ckmnmjb39kjm")))) + "0apgpdnn74mqg2bnr8yjyxgyvdl411h0r2b1r2xd67k21pyxs8bd")))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster))) (home-page "https://cran.r-project.org/web/packages/clue/") -- cgit 1.4.1 From 77dbd8437024998716f2b2233fe40def8d73d0cb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:43 +0000 Subject: gnu: r-sitmo: Update to 2.0.2. * gnu/packages/cran.scm (r-sitmo): Update to 2.0.2. [native-inputs]: Add r-knitr. --- gnu/packages/cran.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f7b76be239..e7222a130b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -19023,16 +19023,18 @@ consensus and secondary clusterings.") (define-public r-sitmo (package (name "r-sitmo") - (version "2.0.1") + (version "2.0.2") (source (origin (method url-fetch) (uri (cran-uri "sitmo" version)) (sha256 (base32 - "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c")))) + "1hm89zi38ldgbskyx1cn7gm87yqy7zrxli8q05a36y1ndvazi3j4")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/coatless/sitmo/") (synopsis "Parallel pseudo random number generator header files") (description -- cgit 1.4.1 From 5c572721565e35de8039afd764f66269eaf770c4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:44 +0000 Subject: gnu: r-systemfonts: Update to 1.0.3. * gnu/packages/cran.scm (r-systemfonts): Update to 1.0.3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e7222a130b..15ccbcb7b2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -19784,14 +19784,14 @@ both R code and compiled C/C++/FORTRAN code.") (define-public r-systemfonts (package (name "r-systemfonts") - (version "1.0.2") + (version "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "systemfonts" version)) (sha256 (base32 - "1a9nzd4nqawr6ni3mw7xc2yq77fb2f91aarnc906mq26510rdb11")))) + "1fmv1ni77ncz6rrm4iv8a7l6pbqnk2ri0yzad2bs943gxbarjz34")))) (properties `((upstream-name . "systemfonts"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 9b64ba34e00ab148b0f5ca9e54eadf65b89e017d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:44 +0000 Subject: gnu: r-terra: Update to 1.4-11. * gnu/packages/cran.scm (r-terra): Update to 1.4-11. [propagated-inputs]: Remove r-raster. --- gnu/packages/cran.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 15ccbcb7b2..fc3f2d4bba 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -19842,14 +19842,14 @@ emphasize hidden group structures in networks or focus on specific nodes.") (define-public r-terra (package (name "r-terra") - (version "1.3-22") + (version "1.4-11") (source (origin (method url-fetch) (uri (cran-uri "terra" version)) (sha256 (base32 - "1z5zql68q4n81ccpl02hndhbavhhqs65bli1hjxlqdwdq192whkh")))) + "08gx28ad00adz4fqch3fx27s6yd0rpjhmdy6b83d1wnlzzgc13qa")))) (properties `((upstream-name . "terra"))) (build-system r-build-system) (inputs @@ -19859,8 +19859,7 @@ emphasize hidden group structures in networks or focus on specific nodes.") ("sqlite" ,sqlite) ; needed for proj ("zlib" ,zlib))) (propagated-inputs - `(("r-raster" ,r-raster) - ("r-rcpp" ,r-rcpp))) + `(("r-rcpp" ,r-rcpp))) (native-inputs `(("pkg-config" ,pkg-config))) (home-page "https://rspatial.org/terra") -- cgit 1.4.1 From 0311f3e5e9db39427d3e66671e666dbd85f473ff Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:44 +0000 Subject: gnu: r-parameters: Update to 0.15.0. * gnu/packages/cran.scm (r-parameters): Update to 0.15.0. [propagated-inputs]: Add r-datawizard. --- gnu/packages/cran.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index fc3f2d4bba..31c3990abc 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -19966,18 +19966,19 @@ in pipelines.") (define-public r-parameters (package (name "r-parameters") - (version "0.14.0") + (version "0.15.0") (source (origin (method url-fetch) (uri (cran-uri "parameters" version)) (sha256 (base32 - "03x2h8izbpz9cq25i0a6dh99m26a9isgpv4kxsfkx97qzlh9cd67")))) + "0f06bwlc1g0xdyhdqzx8plfx1jwk8a9j4lcbl91wjsil8wja0bkl")))) (properties `((upstream-name . "parameters"))) (build-system r-build-system) (propagated-inputs `(("r-bayestestr" ,r-bayestestr) + ("r-datawizard" ,r-datawizard) ("r-insight" ,r-insight))) (native-inputs `(("r-knitr" ,r-knitr))) -- cgit 1.4.1 From 166fdac32a00af417bf070f63d4b8fbd13774bf7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:44 +0000 Subject: gnu: r-desolve: Update to 1.30. * gnu/packages/cran.scm (r-desolve): Update to 1.30. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 31c3990abc..6c3d259350 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -20131,13 +20131,13 @@ programming problems.") (define-public r-desolve (package (name "r-desolve") - (version "1.29") + (version "1.30") (source (origin (method url-fetch) (uri (cran-uri "deSolve" version)) (sha256 - (base32 "02hrd31ky9id7q2bwkj436j4fj4xbs3j9sfmyi1nl7hml5dy2vr6")))) + (base32 "0j7mmg1mimdpql8f4i9dn920ciyyq80a5qnc4fq5xn5lyrx5vxir")))) (properties `((upstream-name . "deSolve"))) (build-system r-build-system) (native-inputs -- cgit 1.4.1 From 9be3daf763ab88452db4879cc274fc3d57cefefc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:45 +0000 Subject: gnu: r-fda: Update to 5.4.0. * gnu/packages/cran.scm (r-fda): Update to 5.4.0. [propagated-inputs]: Add r-desolve. --- gnu/packages/cran.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6c3d259350..5869dfa905 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -22321,18 +22321,19 @@ variable observed over time.") (define-public r-fda (package (name "r-fda") - (version "5.1.9") + (version "5.4.0") (source (origin (method url-fetch) (uri (cran-uri "fda" version)) (sha256 (base32 - "0yjrjsv55bcwqn2yxjgj3hn17wfvjvgngfw9xv3w802i52yz9gf8")))) + "000flssclb2c1sfm2czyp1qxrfrl9rp6bd8sw87ign8165maplqf")))) (properties `((upstream-name . "fda"))) (build-system r-build-system) (propagated-inputs - `(("r-fds" ,r-fds) + `(("r-desolve" ,r-desolve) + ("r-fds" ,r-fds) ("r-matrix" ,r-matrix))) (home-page "https://www.functionaldata.org") (synopsis "Functional data analysis") -- cgit 1.4.1 From cb1ee31bebe1e7c6008997f9569cbbcdab7722e7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:45 +0000 Subject: gnu: r-actuar: Update to 3.2-0. * gnu/packages/cran.scm (r-actuar): Update to 3.2-0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5869dfa905..427d8be293 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -22563,14 +22563,14 @@ API; see the package vignette for details.") (define-public r-actuar (package (name "r-actuar") - (version "3.1-4") + (version "3.2-0") (source (origin (method url-fetch) (uri (cran-uri "actuar" version)) (sha256 (base32 - "0m9b4787a866cddf1skjz6634237dvg1i5qyqss4sgvcrbmx3hw0")))) + "015brjjgmkwmjajdjdw8gs02jrd96if425pk9a97d499hzsq3xds")))) (properties `((upstream-name . "actuar"))) (build-system r-build-system) (propagated-inputs `(("r-expint" ,r-expint))) -- cgit 1.4.1 From 4fc29a0d3da4f36ddeb0314320727d75b7f90527 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:45 +0000 Subject: gnu: r-caret: Update to 6.0-90. * gnu/packages/cran.scm (r-caret): Update to 6.0-90. [propagated-inputs]: Add r-e1071. --- gnu/packages/cran.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 427d8be293..f917647a5f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -22706,17 +22706,18 @@ it may be seen by an animal with less acute vision.") (define-public r-caret (package (name "r-caret") - (version "6.0-88") + (version "6.0-90") (source (origin (method url-fetch) (uri (cran-uri "caret" version)) (sha256 (base32 - "174cyyhsw8s6jp80spmi40qq9sw5ys0r58v4ikp53kiw1dhd247s")))) + "1g36m06hp2fxxwv155bwbqlf97xhcia1lmg3axg6d74kgpns8lg8")))) (build-system r-build-system) (propagated-inputs - `(("r-foreach" ,r-foreach) + `(("r-e1071" ,r-e1071) + ("r-foreach" ,r-foreach) ("r-ggplot2" ,r-ggplot2) ("r-lattice" ,r-lattice) ("r-modelmetrics" ,r-modelmetrics) -- cgit 1.4.1 From 095bac3cb4b56d7641b311d3ba3a970d05c42b78 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:45 +0000 Subject: gnu: r-anthropometry: Update to 1.16. * gnu/packages/cran.scm (r-anthropometry): Update to 1.16. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f917647a5f..00281ad27b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -23036,14 +23036,14 @@ Edition), John Wiley and Sons.") (define-public r-anthropometry (package (name "r-anthropometry") - (version "1.15") + (version "1.16") (source (origin (method url-fetch) (uri (cran-uri "Anthropometry" version)) (sha256 (base32 - "03xw0ggb2qqlldrv0qpjwmncnari742habb46im7y65bhgnr2awx")))) + "0iqlmp9vig4qdavs37kislqxwhk0c0pgsn1kwz3mm75nylxmpbp0")))) (properties `((upstream-name . "Anthropometry"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From d2b49c25b4f69e1e5b98017be32977542dcc63c7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:45 +0000 Subject: gnu: r-msm: Update to 1.6.9. * gnu/packages/cran.scm (r-msm): Update to 1.6.9. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 00281ad27b..4c5b9996ba 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -23963,14 +23963,14 @@ errors; tetrachoric and biserial correlations are special cases.") (define-public r-msm (package (name "r-msm") - (version "1.6.8") + (version "1.6.9") (source (origin (method url-fetch) (uri (cran-uri "msm" version)) (sha256 (base32 - "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk")))) + "08vhazswyxr3y1zb9y60mbg3bappzlizxml8s08p65mh82xxkz5f")))) (properties `((upstream-name . "msm"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 39b793f8f2b1aeb71e21840c8535b2d0bf6face1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:46 +0000 Subject: gnu: r-sem: Update to 3.1-13. * gnu/packages/cran.scm (r-sem): Update to 3.1-13. [propagated-inputs]: Remove r-matrixcalc. --- gnu/packages/cran.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4c5b9996ba..6d1b0b053e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24066,20 +24066,19 @@ actuarial models such as pension mathematics.") (define-public r-sem (package (name "r-sem") - (version "3.1-11") + (version "3.1-13") (source (origin (method url-fetch) (uri (cran-uri "sem" version)) (sha256 (base32 - "03j3ig6fy34pi6nwfq9w8f5m555lilw5skr1vn6ay4yvjmvavc9k")))) + "0r9g4j0w6q4qy9jl9gkjkihml4109ymg3y6zmhyg806q19qryx07")))) (properties `((upstream-name . "sem"))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) ("r-mass" ,r-mass) - ("r-matrixcalc" ,r-matrixcalc) ("r-mi" ,r-mi))) (home-page "https://cran.r-project.org/package=sem") (synopsis "Structural equation models") -- cgit 1.4.1 From 3f8f84719d7a05f2eef280bd4b2760207bd1e691 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:46 +0000 Subject: gnu: r-rpf: Update to 1.0.11. * gnu/packages/cran.scm (r-rpf): Update to 1.0.11. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6d1b0b053e..ab7d36eeca 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24185,14 +24185,14 @@ and analyze Stan models.") (define-public r-rpf (package (name "r-rpf") - (version "1.0.8") + (version "1.0.11") (source (origin (method url-fetch) (uri (cran-uri "rpf" version)) (sha256 (base32 - "039r6yz2ax7i9sv8vi98yg7llwb966ay6mrifpmp6q3xh1f634kl")))) + "1yr1i7kswq57mcxv05lh7bvbicz1djqxcl6f13dlgsf3ww56gzg1")))) (properties `((upstream-name . "rpf"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From a047882ebc77a7a1d9980416bfa91b8eddfa6dbe Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:46 +0000 Subject: gnu: r-qgraph: Update to 1.9. * gnu/packages/cran.scm (r-qgraph): Update to 1.9. [propagated-inputs]: Remove r-dplyr. --- gnu/packages/cran.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ab7d36eeca..2cfe12962e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24377,21 +24377,20 @@ network, tree, dendrogram, and Sankey graphs from R using data frames.") (define-public r-qgraph (package (name "r-qgraph") - (version "1.6.9") + (version "1.9") (source (origin (method url-fetch) (uri (cran-uri "qgraph" version)) (sha256 (base32 - "153bqfmsrghkg7598nfr57r3cxv6dn6ir084njl2sqq5np0sj9di")))) + "1ahhzp64jdgki5p2wga5mn8a2n1x2zldgpilrpf7hy5l9nf4imz1")))) (properties `((upstream-name . "qgraph"))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) ("r-colorspace" ,r-colorspace) ("r-corpcor" ,r-corpcor) - ("r-dplyr" ,r-dplyr) ("r-fdrtool" ,r-fdrtool) ("r-ggplot2" ,r-ggplot2) ("r-glasso" ,r-glasso) -- cgit 1.4.1 From 6c6fc675004dcded000b534f9bfa2479fc79f81b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:46 +0000 Subject: gnu: r-rcdd: Update to 1.4. * gnu/packages/cran.scm (r-rcdd): Update to 1.4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2cfe12962e..2faece18aa 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -25686,14 +25686,14 @@ Mean Test, Durbin-Watson statistic etc.") (define-public r-rcdd (package (name "r-rcdd") - (version "1.2-2") + (version "1.4") (source (origin (method url-fetch) (uri (cran-uri "rcdd" version)) (sha256 (base32 - "0pzpbqnlgzr240iici70278py5wnbbxkzlgn112f9wv5ga3riric")))) + "02jj1lpk4kvjh5484lbdrdlx2ffk9qdxys7afyakd5kl6swqalz2")))) (properties `((upstream-name . "rcdd"))) (build-system r-build-system) -- cgit 1.4.1 From d50963ee1b9c6bbbea93cdf00b6e573883319ad6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:46 +0000 Subject: gnu: r-optimx: Update to 2021-10.12. * gnu/packages/cran.scm (r-optimx): Update to 2021-10.12. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2faece18aa..3e3b8e0565 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -25813,14 +25813,14 @@ estimation.") (define-public r-optimx (package (name "r-optimx") - (version "2021-6.12") + (version "2021-10.12") (source (origin (method url-fetch) (uri (cran-uri "optimx" version)) (sha256 (base32 - "059md564p2pk5nis9kbcn1kw2fw130vg53fxlr5xzpv1c9gfhq3k")))) + "0hvrpfya767vp3anmb8ih516v4zz1sv4h193rn93kyjydf2lqf1r")))) (properties `((upstream-name . "optimx"))) (build-system r-build-system) (propagated-inputs `(("r-numderiv" ,r-numderiv))) -- cgit 1.4.1 From bb3f7c1ae97524a7513fc5376c32923d1eb2b8ea Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:47 +0000 Subject: gnu: r-lightgbm: Update to 3.3.0. * gnu/packages/cran.scm (r-lightgbm): Update to 3.3.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3e3b8e0565..2235d4a19a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -26255,14 +26255,14 @@ input.") (define-public r-lightgbm (package (name "r-lightgbm") - (version "3.2.1") + (version "3.3.0") (source (origin (method url-fetch) (uri (cran-uri "lightgbm" version)) (sha256 (base32 - "1136di7k3gs9kk7vd9bc3mdm0qrx3a546ngar8inmgyhi0zk6pkd")))) + "1sgimzax84rag02gqv2qag2cg8mmhkv71xydawg7bkxk95dycbc2")))) (properties `((upstream-name . "lightgbm"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 2498f757af139647c52441293f4e143884f17bac Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:47 +0000 Subject: gnu: r-memuse: Update to 4.2-1. * gnu/packages/cran.scm (r-memuse): Update to 4.2-1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2235d4a19a..b1c945478b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -26536,13 +26536,13 @@ doi.org/10.1007/s10115-013-0679-x} for details.") (define-public r-memuse (package (name "r-memuse") - (version "4.1-0") + (version "4.2-1") (source (origin (method url-fetch) (uri (cran-uri "memuse" version)) (sha256 (base32 - "1bbjp8y0ji71956fbaxiil7ynq2nkmmgz7i9xps83m3bbp5d3mjq")))) + "1wvwnjaaiv2647561z2b55dss35033ildx4kk8hzxfzgsjmdpsgm")))) (properties `((upstream-name . "memuse"))) (build-system r-build-system) (home-page "https://github.com/shinra-dev/memuse") -- cgit 1.4.1 From 1f552f46ce5e5f1308cca662d03478e43a7baa1c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:47 +0000 Subject: gnu: r-goftest: Update to 1.2-3. * gnu/packages/cran.scm (r-goftest): Update to 1.2-3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b1c945478b..2b1e854e8a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -26625,14 +26625,14 @@ and predictions of any machine learning model. Implemented methods are: (define-public r-goftest (package (name "r-goftest") - (version "1.2-2") + (version "1.2-3") (source (origin (method url-fetch) (uri (cran-uri "goftest" version)) (sha256 (base32 - "0ivnkqhv5xgiv05dm648nngacymd8x8g0fyppv3bc0mhcqk9k5z4")))) + "06bz6k7smr4jbvzmb73qc5fkf4my59w5gbl18wlmpkkymsv78prs")))) (properties `((upstream-name . "goftest"))) (build-system r-build-system) (home-page "https://github.com/baddstats/goftest") -- cgit 1.4.1 From 4ccb7b345ea6c110132d35f8fb81d5d5836fb815 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:47 +0000 Subject: gnu: r-spatstat-geom: Update to 2.3-0. * gnu/packages/cran.scm (r-spatstat-geom): Update to 2.3-0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2b1e854e8a..624d008aa8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -26738,14 +26738,14 @@ package.") (define-public r-spatstat-geom (package (name "r-spatstat-geom") - (version "2.2-2") + (version "2.3-0") (source (origin (method url-fetch) (uri (cran-uri "spatstat.geom" version)) (sha256 (base32 - "0rx28g064641yrk2h23qpyc0bgs20lpsnqmyl1d06530ga6r1qc3")))) + "1iz9zi45nli5lf96ng6bqqbl4ix3zxzlfclkg4cdb9h98nj4c5vv")))) (properties `((upstream-name . "spatstat.geom"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 453ceb8563d90094474edc1649478ed335f6358c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:48 +0000 Subject: gnu: r-exactranktests: Update to 0.8-34. * gnu/packages/cran.scm (r-exactranktests): Update to 0.8-34. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 624d008aa8..9e9e3fcf00 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -27318,14 +27318,14 @@ the @code{survival} package.") (define-public r-exactranktests (package (name "r-exactranktests") - (version "0.8-32") + (version "0.8-34") (source (origin (method url-fetch) (uri (cran-uri "exactRankTests" version)) (sha256 (base32 - "0p7h7w470p5qpsbrhw12zlsshyai56za5dsdva8cf9sikn0955qr")))) + "1i4mwz61mjlh1ai3dww2pjkicx9ww8c4mljnr8xlawh91479lva9")))) (properties `((upstream-name . "exactRankTests"))) (build-system r-build-system) -- cgit 1.4.1 From 2e401e85b5bb9be45a2f5a7cc936fc091ceb2b24 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:48 +0000 Subject: gnu: r-igraph: Update to 1.2.7. * gnu/packages/cran.scm (r-igraph): Update to 1.2.7. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9e9e3fcf00..7c707cfb40 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -27514,14 +27514,14 @@ model.") (define-public r-igraph (package (name "r-igraph") - (version "1.2.6") + (version "1.2.7") (source (origin (method url-fetch) (uri (cran-uri "igraph" version)) (sha256 (base32 - "0vf7wrx77cdiav8724cw8gchrn0y9wvywphf5km4pa7xcqhsf3b4")))) + "1r8vmqm2rq1jnkh8axr4gw1hbj34ca1dil154qp037imfcra1h95")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) -- cgit 1.4.1 From d9b0e009c57ee79aa7a2deca03599736124f64b3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:48 +0000 Subject: gnu: r-workflows: Update to 0.2.4. * gnu/packages/cran.scm (r-workflows): Update to 0.2.4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7c707cfb40..a3d5107214 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -27546,14 +27546,14 @@ more.") (define-public r-workflows (package (name "r-workflows") - (version "0.2.3") + (version "0.2.4") (source (origin (method url-fetch) (uri (cran-uri "workflows" version)) (sha256 (base32 - "0bca4s49qabam4ny8vckxcghj3z0xfhwfhs5h1136kihrr5pm6mw")))) + "1sxrgza922p137z41jcj2iwk19lxzwh6kp4kz7h9kw0b8rvfqwab")))) (properties `((upstream-name . "workflows"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 5643a559473b81e3ba97424490eded3540ce94c1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:48 +0000 Subject: gnu: r-tidytext: Update to 0.3.2. * gnu/packages/cran.scm (r-tidytext): Update to 0.3.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a3d5107214..0ce6116318 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -28061,14 +28061,14 @@ vignettes in all common formats.") (define-public r-tidytext (package (name "r-tidytext") - (version "0.3.1") + (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "tidytext" version)) (sha256 (base32 - "182gad5pzz6zvhbla3d496sxwiszc1qz8kzzkksaacwpsrc61f9h")))) + "0as7lscjl6ywk85almmb4f71vxmgkfds46g52ryggkg2isksvq3g")))) (properties `((upstream-name . "tidytext"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From a365fcbc9c80b4737258a483ee3ccf4f3aba2490 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:48 +0000 Subject: gnu: r-tidymodels: Update to 0.1.4. * gnu/packages/cran.scm (r-tidymodels): Update to 0.1.4. [propagated-inputs]: Add r-hardhat. --- gnu/packages/cran.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0ce6116318..d49b6e2139 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -28214,14 +28214,14 @@ use.") (define-public r-tidymodels (package (name "r-tidymodels") - (version "0.1.3") + (version "0.1.4") (source (origin (method url-fetch) (uri (cran-uri "tidymodels" version)) (sha256 (base32 - "18vz0xsgxrfzcfxpvilhj1w0f4v4lx5ws37nwmy40lhv3v05nxn8")))) + "18krycdn0h1i8swrq6bgj8qnb200rr0pqhr6maq3h1jc66x0y7nd")))) (properties `((upstream-name . "tidymodels"))) (build-system r-build-system) (propagated-inputs @@ -28231,6 +28231,7 @@ use.") ("r-dials" ,r-dials) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) + ("r-hardhat" ,r-hardhat) ("r-infer" ,r-infer) ("r-modeldata" ,r-modeldata) ("r-parsnip" ,r-parsnip) -- cgit 1.4.1 From 00fd3499752f1928b59dd74fac5fab198b5d90af Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:49 +0000 Subject: gnu: r-perm: Update to 1.0-0.2. * gnu/packages/cran.scm (r-perm): Update to 1.0-0.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d49b6e2139..d2a5cae519 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -28390,14 +28390,14 @@ including: (define-public r-perm (package (name "r-perm") - (version "1.0-0.0") + (version "1.0-0.2") (source (origin (method url-fetch) (uri (cran-uri "perm" version)) (sha256 (base32 - "0075awl66ynv10vypg63fcxk33qzvxddrp8mi4w08ysvimcyxijk")))) + "182ac1y91yzb34zwdcmx5fdfr5z0cha0gx2bgk36gwxhgfc994kj")))) (properties `((upstream-name . "perm"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/perm/") -- cgit 1.4.1 From f006a089915cdeef420ce46d2d8ae535d67bacd0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:49 +0000 Subject: gnu: r-qtl: Update to 1.50. * gnu/packages/cran.scm (r-qtl): Update to 1.50. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d2a5cae519..7b68bd86b3 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -28413,14 +28413,14 @@ covariate (usually group indicator) and the scores.") (define-public r-qtl (package (name "r-qtl") - (version "1.48-1") + (version "1.50") (source (origin (method url-fetch) (uri (cran-uri "qtl" version)) (sha256 (base32 - "098mgmfj8ndi8yipr9b3f6gbbh78cgp9j7y561nlnhrnyc8bsih9")))) + "1mcy9wlp5lj5f3z4mf3n5li7x32vj67rmhjnzsp8fhfw0ipnaf1d")))) (build-system r-build-system) (home-page "https://rqtl.org/") (synopsis "R package for analyzing QTL experiments in genetics") -- cgit 1.4.1 From 7494bac6213180d8c3fa136e6dd0f4ba534d4adc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:49 +0000 Subject: gnu: r-qtl2: Update to 0.28. * gnu/packages/cran.scm (r-qtl2): Update to 0.28. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7b68bd86b3..d41f1c3734 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -28436,12 +28436,12 @@ genome scans.") (define-public r-qtl2 (package (name "r-qtl2") - (version "0.24") + (version "0.28") (source (origin (method url-fetch) (uri (cran-uri "qtl2" version)) (sha256 - (base32 "1558khh0zkwm0rdk87krv9836krvwv5h7ymlz9bsrgcvypyr9186")))) + (base32 "0ppc6dzlq77mppxc6bczai9gi40jrbxd1466y2cn2s8a4ah1jg9y")))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table) -- cgit 1.4.1 From 06b820105ef615ff840589a3a0a2335eea3099b6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:49 +0000 Subject: gnu: r-seurat: Update to 4.0.5. * gnu/packages/cran.scm (r-seurat): Update to 4.0.5. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d41f1c3734..ab47f96c37 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -28563,13 +28563,13 @@ other R users.") (define-public r-seurat (package (name "r-seurat") - (version "4.0.4") + (version "4.0.5") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "1pa2v29mx39swblzwzqc7rpql2rizhi2nj426r1i63wyla6lcxc0")))) + "18svlpfbgs5vdzw2jyg99kj0jacag6dwwhjdg1zpmrh0fm0praxg")))) (properties `((upstream-name . "Seurat"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 80bcd91076f8bdcec1f07a3309ae80f3de989fb5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:50 +0000 Subject: gnu: r-decon: Update to 1.3-4. * gnu/packages/cran.scm (r-decon): Update to 1.3-4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ab47f96c37..cb482aea11 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -28764,14 +28764,14 @@ parabolic or user defined by custom scale factors.") (define-public r-decon (package (name "r-decon") - (version "1.2-4") + (version "1.3-4") (source (origin (method url-fetch) (uri (cran-uri "decon" version)) (sha256 (base32 - "1v4l0xq29rm8mks354g40g9jxn0didzlxg3g7z08m0gvj29zdj7s")))) + "036cv56wf42q2p3d5h15hbrp5rc29xxy20qwv4k1qzhkq6hmw0qs")))) (properties `((upstream-name . "decon"))) (build-system r-build-system) (native-inputs -- cgit 1.4.1 From ad8043821a017f344968873dc36451c036c065b3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:50 +0000 Subject: gnu: r-textshaping: Update to 0.3.6. * gnu/packages/cran.scm (r-textshaping): Update to 0.3.6. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index cb482aea11..ffff509013 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -29382,14 +29382,14 @@ clusterings as resolution increases.") (define-public r-textshaping (package (name "r-textshaping") - (version "0.3.5") + (version "0.3.6") (source (origin (method url-fetch) (uri (cran-uri "textshaping" version)) (sha256 (base32 - "06bdc5wxvgv38fnzpyjj9p62ifpfshaangkn96gw05yxn11s46h0")))) + "1niaj1dh09rqrg9hrh98ddnc0f2nkyq9iizv24lcwm9gjs3w1ql0")))) (properties `((upstream-name . "textshaping"))) (build-system r-build-system) (inputs -- cgit 1.4.1 From b774be8a60f9c9705f612c5a7b405cef78845a04 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:50 +0000 Subject: gnu: r-lwgeom: Update to 0.2-8. * gnu/packages/cran.scm (r-lwgeom): Update to 0.2-8. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ffff509013..6e5b89a230 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -30083,14 +30083,14 @@ and formatted text files with additional meta-data, such including @code{.csv}, (define-public r-lwgeom (package (name "r-lwgeom") - (version "0.2-7") + (version "0.2-8") (source (origin (method url-fetch) (uri (cran-uri "lwgeom" version)) (sha256 (base32 - "1qgszbw03haqfjdc07ivkg8r0yd50ldkiqq27ppkaibw7mgiak5k")))) + "0d4b1djwrzla91mmyya2m1250mb44fzmq3d36w5mk81d4bg952pl")))) (properties `((upstream-name . "lwgeom"))) (build-system r-build-system) (inputs -- cgit 1.4.1 From b8cd476693df80acf79e3ebb25a3d757bc2e3148 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:50 +0000 Subject: gnu: r-textplot: Update to 0.2.1. * gnu/packages/cran.scm (r-textplot): Update to 0.2.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6e5b89a230..95504b8b29 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -30413,14 +30413,14 @@ quantitative real-time polymerase chain reaction (qPCR).") (define-public r-textplot (package (name "r-textplot") - (version "0.2.0") + (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "textplot" version)) (sha256 (base32 - "1fhnwbcgkliq71lry21762djhlbap1qg4mgil0np46aa6619l21m")))) + "10nxh9axhy6kyp6f3rz7smq08yl35ydx9jx47bs7i0bmcl2kwxvl")))) (properties `((upstream-name . "textplot"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From a4ddc61806fbd7810be7b67c2f875dbb3c7d1c50 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:51 +0000 Subject: gnu: r-exactextractr: Update to 0.7.1. * gnu/packages/cran.scm (r-exactextractr): Update to 0.7.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 95504b8b29..e50d76cbac 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -30796,14 +30796,14 @@ Apache2.") (define-public r-exactextractr (package (name "r-exactextractr") - (version "0.7.0") + (version "0.7.1") (source (origin (method url-fetch) (uri (cran-uri "exactextractr" version)) (sha256 (base32 - "1fwbl0rn0990cs2rvvwjbflp9mall6hjkindpjmdcy6qafiviid6")))) + "1gc1p9pgazhblk8jgykxxjpblylbaq5r9hdlw3ilz5g45yjjwcnc")))) (properties `((upstream-name . "exactextractr"))) (build-system r-build-system) (inputs `(("geos" ,geos))) -- cgit 1.4.1 From e50595af5098b96162e76875fbbdfa5349fd608e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:51 +0000 Subject: gnu: r-stringfish: Update to 0.15.4. * gnu/packages/cran.scm (r-stringfish): Update to 0.15.4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e50d76cbac..d00649439b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -30824,14 +30824,14 @@ the @code{raster} package that is suitable for extracting raster values using (define-public r-stringfish (package (name "r-stringfish") - (version "0.15.2") + (version "0.15.4") (source (origin (method url-fetch) (uri (cran-uri "stringfish" version)) (sha256 (base32 - "0m8485p1gb5z2n2g5nyr38zixw4iv8xxm7bxspxlxvx6alhn03pn")))) + "1n67y9vgv8vb8qd091d1wm5sgbalcm2avh2fz0hd3mmglpkr83wf")))) (properties `((upstream-name . "stringfish"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 745dac9391acb22fa876905e64e3d15da50cb31d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:51 +0000 Subject: gnu: r-keras: Update to 2.6.1. * gnu/packages/cran.scm (r-keras): Update to 2.6.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d00649439b..dade3b6efe 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31015,14 +31015,14 @@ between them.") (define-public r-keras (package (name "r-keras") - (version "2.6.0") + (version "2.6.1") (source (origin (method url-fetch) (uri (cran-uri "keras" version)) (sha256 (base32 - "1pgdcypp9x9dw7aa5ka7qqgd24jdcp3ja94jpm7j6l6j4930k5vd")))) + "0xg4n9sp1pf2yfbba3lb3fzr5gbdwlhv4j1h5njfqmjy5984b8ij")))) (properties `((upstream-name . "keras"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From f8e998d9aa9e30aeec1f155788d0a8f9bbc6d159 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:51 +0000 Subject: gnu: r-ztpln: Update to 0.1.2. * gnu/packages/cran.scm (r-ztpln): Update to 0.1.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index dade3b6efe..a44cac1b51 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31127,14 +31127,14 @@ Bessel K function.") (define-public r-ztpln (package (name "r-ztpln") - (version "0.1.1") + (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "ztpln" version)) (sha256 (base32 - "18rbfdp22jaxg4nkqzj2393nhjdl1gzv4xhmr6aci76ymdixsfnl")))) + "1b22m72a8117yrgq5k1gzsrbx6yrsrj7bpd49lh7x3vbaz56c0wr")))) (properties `((upstream-name . "ztpln"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From ccc23f0e59dc54092c7a1e17a9fcd8f858dffd43 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:51 +0000 Subject: gnu: r-dismo: Update to 1.3-5. * gnu/packages/cran.scm (r-dismo): Update to 1.3-5. [propagated-inputs]: Add r-terra. --- gnu/packages/cran.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a44cac1b51..25f76a2cac 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31234,20 +31234,21 @@ to archive and assign DOIs to data, software, figures, and more.") (define-public r-dismo (package (name "r-dismo") - (version "1.3-3") + (version "1.3-5") (source (origin (method url-fetch) (uri (cran-uri "dismo" version)) (sha256 (base32 - "1jj9d78f251bxgrwbv1ycn677qnhvl40bfan12x8fhlaq4d36rgx")))) + "1rqf6h4imbqvs7hjd1k4my6154wg0qnmnp5byan403rcshr1jbl1")))) (properties `((upstream-name . "dismo"))) (build-system r-build-system) (propagated-inputs `(("r-raster" ,r-raster) ("r-rcpp" ,r-rcpp) - ("r-sp" ,r-sp))) + ("r-sp" ,r-sp) + ("r-terra" ,r-terra))) (home-page "https://rspatial.org/raster/sdm/") (synopsis "Species distribution modeling") (description -- cgit 1.4.1 From 9a54f60ba32d5a3f8730e60c84ad3d3e3c691edf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:52 +0000 Subject: gnu: r-paws-common: Update to 0.3.13. * gnu/packages/cran.scm (r-paws-common): Update to 0.3.13. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 25f76a2cac..66ff3366e2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31295,14 +31295,14 @@ fully reproducible.") (define-public r-paws-common (package (name "r-paws-common") - (version "0.3.12") + (version "0.3.13") (source (origin (method url-fetch) (uri (cran-uri "paws.common" version)) (sha256 (base32 - "1khq1rv0yij4l0vi2x6hslnzpsd6m5n6nipfac7g3na9ah93h8i9")))) + "15sj7yw4hj76minr00xhgzkg1rwb7gsr2ib9q4d053i5f3jcy54a")))) (properties `((upstream-name . "paws.common"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From fb735f7de99bd6401b1a0321834e8dfbd4782b20 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:52 +0000 Subject: gnu: r-logger: Update to 0.2.2. * gnu/packages/cran.scm (r-logger): Update to 0.2.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 66ff3366e2..0d87285e7a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -32125,13 +32125,13 @@ Monte Carlo approach implemented in JAGS.") (define-public r-logger (package (name "r-logger") - (version "0.2.1") + (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "logger" version)) (sha256 - (base32 "0p607da2rdrfj9sbrrq9hpqp26nyj3imd1590c13bxskqfhv0sz8")))) + (base32 "08kym5i5fvbf5xhh9qdszp4jdgyc7j7zpnwzy68wabqz73aff6sg")))) (properties `((upstream-name . "logger"))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) -- cgit 1.4.1 From b2245f66f678b02f489465a593b48c47d06706a7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:52 +0000 Subject: gnu: r-mgcv: Update to 1.8-38. * gnu/packages/statistics.scm (r-mgcv): Update to 1.8-38. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 7f1460b089..d4ce9d6cfc 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -638,13 +638,13 @@ nonlinear mixed-effects models.") (define-public r-mgcv (package (name "r-mgcv") - (version "1.8-37") + (version "1.8-38") (source (origin (method url-fetch) (uri (cran-uri "mgcv" version)) (sha256 - (base32 "14gw714xcyvgrbajijmyd4v8zs84i701g7gyld6z8p7677dgc8w8")))) + (base32 "1fyx8b0xjyx75mp90v314gayzydkca5y90p76jnwxzfnhxbys4nd")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix) -- cgit 1.4.1 From 0178f11814dca4b0e0e125b7a6638f75d83700d3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:52 +0000 Subject: gnu: r-stringi: Update to 1.7.5. * gnu/packages/statistics.scm (r-stringi): Update to 1.7.5. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index d4ce9d6cfc..9c8794d6fe 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1047,14 +1047,14 @@ solution for sending email, including attachments, from within R.") (define-public r-stringi (package (name "r-stringi") - (version "1.7.4") + (version "1.7.5") (source (origin (method url-fetch) (uri (cran-uri "stringi" version)) (sha256 (base32 - "1mda4612sc573zabsvygnla3vpnf3mql58fc9j450540h6hlwfv2")))) + "0r959gzyqkq9683qdfy95g9plwpj3c73n9lhf0a6byybw4scq519")))) (build-system r-build-system) (inputs `(("icu4c" ,icu4c))) (native-inputs `(("pkg-config" ,pkg-config))) -- cgit 1.4.1 From 4ea639a14a1ce486e715ff333ddd1033583d3709 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:52 +0000 Subject: gnu: r-mime: Update to 0.12. * gnu/packages/statistics.scm (r-mime): Update to 0.12. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 9c8794d6fe..c44130c749 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1386,13 +1386,13 @@ supported via Andre Simon's highlight package.") (define-public r-mime (package (name "r-mime") - (version "0.11") + (version "0.12") (source (origin (method url-fetch) (uri (cran-uri "mime" version)) (sha256 (base32 - "1h7fz0rqnp970r9q0d95qcxpxm9mb98rqhcdncx0w2qdkyj2fm11")))) + "0j9qbq9jfsp61h2d0xmb87pa2wi8nhb1h2wih7l5drf1sr8i0059")))) (build-system r-build-system) (home-page "https://github.com/yihui/mime") (synopsis "R package to map filenames to MIME types") -- cgit 1.4.1 From 0ee5a2c17042be6238f5bfc4bb2fa0034f798030 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:52 +0000 Subject: gnu: r-knitr: Update to 1.36. * gnu/packages/statistics.scm (r-knitr): Update to 1.36. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index c44130c749..585875c38f 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1449,13 +1449,13 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.") (define-public r-knitr (package (name "r-knitr") - (version "1.34") + (version "1.36") (source (origin (method url-fetch) (uri (cran-uri "knitr" version)) (sha256 (base32 - "0p6jdicyqknrqilcjm2h4r6vza5lpzccnsdirj92jb3ljg10b0by")))) + "0hcf5gii0qlvv15f86y6h08qp0hd9lcrykzj0mdfjdfi52sgbkkf")))) (build-system r-build-system) (propagated-inputs `(("r-evaluate" ,r-evaluate) -- cgit 1.4.1 From da7d8aab1cb818bcce638023326792e02d68e91c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:53 +0000 Subject: gnu: r-testthat: Update to 3.1.0. * gnu/packages/statistics.scm (r-testthat): Update to 3.1.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 585875c38f..073ad96cfb 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1602,13 +1602,13 @@ R packages that praise their users.") (define-public r-testthat (package (name "r-testthat") - (version "3.0.4") + (version "3.1.0") (source (origin (method url-fetch) (uri (cran-uri "testthat" version)) (sha256 (base32 - "0iqizv2gpv9fg766qv8hbkmc6c5i9xcfrmq9k5m2550p28zff2w3")))) + "11s98q0gm37z1cqzwvdm9pq26v0zbdq9vc5ssl1nsxhsi42v2577")))) (build-system r-build-system) (propagated-inputs `(("r-brio" ,r-brio) -- cgit 1.4.1 From 34244f64dfb375ad88174b8ae19a9dff449b9088 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:53 +0000 Subject: gnu: r-rlang: Update to 0.4.12. * gnu/packages/statistics.scm (r-rlang): Update to 0.4.12. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 073ad96cfb..23b0bcf5db 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1664,13 +1664,13 @@ defined in different packages.") (define-public r-rlang (package (name "r-rlang") - (version "0.4.11") + (version "0.4.12") (source (origin (method url-fetch) (uri (cran-uri "rlang" version)) (sha256 (base32 - "1pfm24jjkxzdb5qcbc05dcjxyk69zpfr5jv4xakqh1xh41mr43kl")))) + "05cr08smr8dlk10m810rw4qi1yhgnny83rwkxib0l4my71br29ia")))) (build-system r-build-system) (home-page "http://rlang.tidyverse.org") (synopsis "Functions for base types, core R and Tidyverse features") -- cgit 1.4.1 From 56703a6a1eb5ecbe9dda07a76e43c5466287713d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:53 +0000 Subject: gnu: r-tibble: Update to 3.1.5. * gnu/packages/statistics.scm (r-tibble): Update to 3.1.5. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 23b0bcf5db..6fbcb56b1a 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1682,14 +1682,14 @@ like tidy evaluation.") (define-public r-tibble (package (name "r-tibble") - (version "3.1.4") + (version "3.1.5") (source (origin (method url-fetch) (uri (cran-uri "tibble" version)) (sha256 (base32 - "0zqpg2haph0qi1x5r6wr083xckab9gw21jbr9spcr8xdf43hx1vk")))) + "1ryv1r3cah1s8dyqdhcb0yl81r384jvgc4d1q9zwsrrsd2x8fqys")))) (build-system r-build-system) (propagated-inputs `(("r-ellipsis" ,r-ellipsis) -- cgit 1.4.1 From 9f466180441c723a7f15cee613224f2f59a71f54 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:53 +0000 Subject: gnu: r-data-table: Update to 1.14.2. * gnu/packages/statistics.scm (r-data-table): Update to 1.14.2. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 6fbcb56b1a..3f979c390d 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1870,13 +1870,13 @@ times.") (define-public r-data-table (package (name "r-data-table") - (version "1.14.0") + (version "1.14.2") (source (origin (method url-fetch) (uri (cran-uri "data.table" version)) (sha256 (base32 - "0kgbvap5v2spnkz3dwfm4jh4qcpvbzdn9s8bzfnhzabz9qjdxw8k")))) + "0arx5wna0sh0vf5q8rjhh8nqdmnvg2pdpbhljl9l0x4kwm8vjhgp")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) -- cgit 1.4.1 From d2cabb2474d542553b27e6a04c9c36588f77c3c9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:53 +0000 Subject: gnu: r-desc: Update to 1.4.0. * gnu/packages/statistics.scm (r-desc): Update to 1.4.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 3f979c390d..5de2ef31e6 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2284,14 +2284,14 @@ module, Java Server Pages, and Python's psp module.") (define-public r-desc (package (name "r-desc") - (version "1.3.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "desc" version)) (sha256 (base32 - "1sw4vya3l971gpccq4gnjywgbl73bgx8la18l0wy617qv94f905y")))) + "0jfnwn1kpiill8v4hmzdk90yz4gk2ha0prr2p0hq36s40v3y8842")))) (build-system r-build-system) (propagated-inputs `(("r-crayon" ,r-crayon) -- cgit 1.4.1 From b3d04cd11ee2bb9ad3b12d9c82f4ddb82347c8d0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:53 +0000 Subject: gnu: r-readr: Update to 2.0.2. * gnu/packages/statistics.scm (r-readr): Update to 2.0.2. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 5de2ef31e6..5e69b29e06 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2557,13 +2557,13 @@ time-of-day values, based on the @code{difftime} class.") (define-public r-readr (package (name "r-readr") - (version "2.0.1") + (version "2.0.2") (source (origin (method url-fetch) (uri (cran-uri "readr" version)) (sha256 (base32 - "0cj5k3ykkhixgdsqm1gnmpc0d8z04l3fhvm2dr5xp7cpmhgsrpfr")))) + "05bnvcc55i0xjilfrqx3700mwiz8sgihq1wxlbvvr8nxa7bmxc4q")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) -- cgit 1.4.1 From 66767856a3b5ca9c33b35207a71cda0aaced6986 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:53 +0000 Subject: gnu: r-rcpparmadillo: Update to 0.10.7.0.0. * gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.10.7.0.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 5e69b29e06..aad8139d3c 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2650,13 +2650,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.10.6.0.0") + (version "0.10.7.0.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "1bcx8fk5l5mmwb6cw36ndvld9v3amkz6vyc19059dw0xp7mxx04v")))) + "1x35xb5yfslsdpaz9msl5p9f7gilnbkhwvq7pbycwasvkp2fma01")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From af55b6c7f5aefb3b5779d3107ced39e9bbb5f5e2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:53 +0000 Subject: gnu: r-mvtnorm: Update to 1.1-3. * gnu/packages/statistics.scm (r-mvtnorm): Update to 1.1-3. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index aad8139d3c..6e4bdb64ae 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4002,13 +4002,13 @@ vignettes.") (define-public r-mvtnorm (package (name "r-mvtnorm") - (version "1.1-2") + (version "1.1-3") (source (origin (method url-fetch) (uri (cran-uri "mvtnorm" version)) (sha256 (base32 - "05wh7mprf2sim2kxh3d72pdcmml6vbikzxavws1dq6mxwlsy2p7j")))) + "0j14q2bkc14v35s5k03sw44zsssrd2qjljlwzj014qxs74hk0kpz")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) -- cgit 1.4.1 From e49de81b3dce8c7f9b66d3162a5a1f2ac137ef5c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:54 +0000 Subject: gnu: r-viridis: Update to 0.6.2. * gnu/packages/statistics.scm (r-viridis): Update to 0.6.2. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 6e4bdb64ae..9b66b2f2cc 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4050,13 +4050,13 @@ memory usage.") (define-public r-viridis (package (name "r-viridis") - (version "0.6.1") + (version "0.6.2") (source (origin (method url-fetch) (uri (cran-uri "viridis" version)) (sha256 (base32 - "1fyax36ycjiypcnxhrv58pq67qv03vfg4lx822d38jpjly54q128")))) + "048kwhbhd49g86cq11fl7vm0whwhjl5gs9xjn040lwcjv78qrdb9")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) -- cgit 1.4.1 From f86e6061554060c18a7b1af90bc100d0582509db Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:54 +0000 Subject: gnu: r-tidyr: Update to 1.1.4. * gnu/packages/statistics.scm (r-tidyr): Update to 1.1.4. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 9b66b2f2cc..8efaa65f67 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4134,14 +4134,14 @@ selection.") (define-public r-tidyr (package (name "r-tidyr") - (version "1.1.3") + (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "tidyr" version)) (sha256 (base32 - "0cpbrvr759z8p7r9lpkjhj2dcdymsbnaib0rma9b4jb7i3qzmh2a")))) + "0h8jfsmn4r7zgfyjmg2qkjd54n0sncq07xjh4mdf2cx4k2z9h30b")))) (build-system r-build-system) (propagated-inputs `(("r-cpp11" ,r-cpp11) -- cgit 1.4.1 From ee8094c640b6a7358fba16477b6b216a0f802439 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:54 +0000 Subject: gnu: r-plotly: Update to 4.10.0. * gnu/packages/statistics.scm (r-plotly): Update to 4.10.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 8efaa65f67..fbf0c0524d 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4219,13 +4219,13 @@ features present in other programming languages.") (define-public r-plotly (package (name "r-plotly") - (version "4.9.4.1") + (version "4.10.0") (source (origin (method url-fetch) (uri (cran-uri "plotly" version)) (sha256 (base32 - "1q711c0lg0jmzrmcc2fhjy70ms49as7cakdbgbh2ij9s149fa7iq")))) + "16iqj7sv49mva6siibsci7iijsbnk7pqvfns9al0k35w9mjmr6dx")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) -- cgit 1.4.1 From 34a9cca76cb3b1b2adcca5811f9c0966bfa03ca0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:54 +0000 Subject: gnu: r-hmisc: Update to 4.6-0. * gnu/packages/statistics.scm (r-hmisc): Update to 4.6-0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index fbf0c0524d..9ffd441041 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4422,13 +4422,13 @@ package instead.") (define-public r-hmisc (package (name "r-hmisc") - (version "4.5-0") + (version "4.6-0") (source (origin (method url-fetch) (uri (cran-uri "Hmisc" version)) (sha256 - (base32 "11qj73zj16p113jpwn2vv06l99kqlcxcmrldbpyi5s7pwing9jnx")))) + (base32 "1bd1c8sichyijprfpnqj5g72nmgs9jvi0zyw8v4nsg1kn83fj71c")))) (properties `((upstream-name . "Hmisc"))) (build-system r-build-system) (native-inputs -- cgit 1.4.1 From a0f8df49dca2a7ef83ce92a8aed7988397436ed5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:54 +0000 Subject: gnu: r-ztable: Update to 0.2.3. * gnu/packages/statistics.scm (r-ztable): Update to 0.2.3. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 9ffd441041..5106bccff0 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4683,13 +4683,13 @@ mechanism.") (define-public r-ztable (package (name "r-ztable") - (version "0.2.2") + (version "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "ztable" version)) (sha256 (base32 - "0wxcdb7yp2r6w5iznz1k49npp5sn4jiybfcj30s3198hkcnv0r8y")))) + "1ps7ix0hc84s0p0ra6bkjxky3cffs1rvdcagqzj78lbdq22dk5j8")))) (build-system r-build-system) (propagated-inputs `(("r-flextable" ,r-flextable) -- cgit 1.4.1 From ca6798d7d32a6d9d1855832089101277ad590714 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:54 +0000 Subject: gnu: r-robustbase: Update to 0.93-9. * gnu/packages/statistics.scm (r-robustbase): Update to 0.93-9. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 5106bccff0..50d9b1c5d1 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5173,14 +5173,14 @@ can be efficiently implemented directly in the R language.") (define-public r-robustbase (package (name "r-robustbase") - (version "0.93-8") + (version "0.93-9") (source (origin (method url-fetch) (uri (cran-uri "robustbase" version)) (sha256 (base32 - "16fmnk3p32mi70rkx89l1v4pry3gnrpy9jicnlfnk6lg1pwz5j8w")))) + "0i9wf4aq8zpn2np6z2rjja21ks9n740dgkiv0qfwdzk3ah3vapyp")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) -- cgit 1.4.1 From b36fc719536d01f63856ebce30b47773dddd543d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 1 Nov 2021 20:44:54 +0000 Subject: gnu: r-lubridate: Update to 1.8.0. * gnu/packages/statistics.scm (r-lubridate): Update to 1.8.0. [propagated-inputs]: Remove r-rcpp; add r-cpp11. --- gnu/packages/statistics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 50d9b1c5d1..bad2e774e1 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5886,18 +5886,18 @@ is supported.") (define-public r-lubridate (package (name "r-lubridate") - (version "1.7.10") + (version "1.8.0") (source (origin (method url-fetch) (uri (cran-uri "lubridate" version)) (sha256 (base32 - "1s653d6rnpf9bkynxmbq4fdjdcz7r9ma19aph8f5y9ck70his4hm")))) + "199b00cql07gf3rf4hh5ba34amnk0ai40zhx73dq1mpkn7ynxml7")))) (build-system r-build-system) (propagated-inputs `(("r-generics" ,r-generics) - ("r-rcpp" ,r-rcpp))) + ("r-cpp11" ,r-cpp11))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/lubridate/") -- cgit 1.4.1 From 4f9f2539f33722dea184100270262420e4029045 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Thu, 28 Oct 2021 17:12:04 +0200 Subject: gnu: Add r-zellkonverter. * gnu/packages/bioconductor.scm (r-zellkonverter): New variable. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 75f6c877b4..936be1476a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4682,6 +4682,38 @@ and specific in detecting differential transcription.") libraries for systems that do not have these available via other means.") (license license:artistic2.0))) +(define-public r-zellkonverter + (package + (name "r-zellkonverter") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "zellkonverter" version)) + (sha256 + (base32 "1ihp2f23lpdfgf3qliy22vrq8czm353hyhqf74r5r712190k6pgg")))) + (properties `((upstream-name . "zellkonverter"))) + (build-system r-build-system) + (propagated-inputs + `(("r-basilisk" ,r-basilisk) + ("r-cli" ,r-cli) + ("r-delayedarray" ,r-delayedarray) + ("r-matrix" ,r-matrix) + ("r-reticulate" ,r-reticulate) + ("r-s4vectors" ,r-s4vectors) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/theislab/zellkonverter") + (synopsis "Conversion between AnnData and single-cell experiments objects") + (description + "This package provides methods to convert between Python AnnData objects +and SingleCellExperiment objects. These are primarily intended for use by +downstream Bioconductor packages that wrap Python methods for single-cell data +analysis. It also includes functions to read and write H5AD files used for +saving AnnData objects to disk.") + (license license:expat))) + (define-public r-geneplotter (package (name "r-geneplotter") -- cgit 1.4.1 From 3c3d7f04100a1634ae5ea2b37a59e1cebcbbfdd2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 2 Nov 2021 16:06:34 +0000 Subject: gnu: r-biocthis: Set HOME variable. * gnu/packages/bioconductor.scm (r-biocthis)[arguments]: Add build phase 'set-HOME. --- gnu/packages/bioconductor.scm | 5 +++++ 1 file changed, 5 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 936be1476a..ab853cf64d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14183,6 +14183,11 @@ Python environments in a single R session.") "08awghsg7q22csb0j9dr8dpb1vkn9gcs9qnhhljxifkw2ahbqia4")))) (properties `((upstream-name . "biocthis"))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs `(("r-biocmanager" ,r-biocmanager) ("r-fs" ,r-fs) -- cgit 1.4.1 From d54a4285ea92f899ad5a0309de9215447139fe5f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 3 Nov 2021 08:14:56 +0000 Subject: gnu: bedtools-2.18: Fix build with newer toolchain. * gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Add phase 'compatibility, fixing syntax quirks that are problematic with newer toolchains. [native-inputs]: Do not inherit. [inherit]: Do not inherit. --- gnu/packages/bioinformatics.scm | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fbcd571c59..a731b9af06 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -544,14 +544,26 @@ BED, GFF/GTF, VCF.") '(#:test-target "test" #:phases (modify-phases %standard-phases + (add-after 'unpack 'compatibility + (lambda _ + (substitute* "src/utils/fileType/FileRecordTypeChecker.h" + (("static const float PERCENTAGE") + "static constexpr float PERCENTAGE")) + (substitute* "src/utils/general/DualQueue.h" + (("template class CompareFunc>") + "template class CompareFunc>")))) (delete 'configure) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) (for-each (lambda (file) (install-file file bin)) - (find-files "bin" ".*"))) - #t))))))) + (find-files "bin" ".*")))))))) + (native-inputs + `(("python" ,python-wrapper))) + (inputs + `(("samtools" ,samtools) + ("zlib" ,zlib))))) (define-public pbbam (package -- cgit 1.4.1 From 0bb9c9a723c1e4178c00a48f175209da85d1e15c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 3 Nov 2021 11:37:16 +0000 Subject: gnu: r-annotationforge: Update to 1.34.1. * gnu/packages/bioconductor.scm (r-annotationforge): Update to 1.34.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ab853cf64d..3bff466fd3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2082,14 +2082,14 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.34.0") + (version "1.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "1by3diy0y4809k97cw97mp4j177gn1dzhqil8myij1r7b8sk7hax")))) + "0g75b2adak87raw0vn20fjh5980y7svknh8ih1sn4fwryglp4ggg")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) -- cgit 1.4.1 From 218912f6ad9c91ac10e6a02ee2c024cb3e87d3dc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 3 Nov 2021 11:37:21 +0000 Subject: gnu: r-annotationhub: Update to 3.0.2. * gnu/packages/bioconductor.scm (r-annotationhub): Update to 3.0.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3bff466fd3..0acdefb28e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2114,14 +2114,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "3.0.1") + (version "3.0.2") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "12i8lafy1z97gs4knqi7r5l1hd7dr6j8a23qj4fkdpqsdpyz21z7")))) + "09drr13qqdj7b711axmlxv2gkaw17cvkhl0g2rh7w0b2vx13fg7y")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From b4888a5581fc4248b0ceadc56350b9b148495bc8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 3 Nov 2021 11:37:21 +0000 Subject: gnu: r-genefilter: Update to 1.74.1. * gnu/packages/bioconductor.scm (r-genefilter): Update to 1.74.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0acdefb28e..a03ed6453f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2929,14 +2929,14 @@ analysis using other methods.") (define-public r-genefilter (package (name "r-genefilter") - (version "1.74.0") + (version "1.74.1") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "0dy9pmlb0pc9b4ks5fb9zgnmhc9f2mkqmsdlb7f5z88xmj68y4qk")))) + "0lsh6akhqm1fadxr7066rcx5y7rnd020icx2cq0bfpymz6ajzsvx")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran) -- cgit 1.4.1 From 11cf6d399cc5aa65519737b76a58c8b5629d743a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 3 Nov 2021 11:37:21 +0000 Subject: gnu: r-dose: Update to 3.18.3. * gnu/packages/bioconductor.scm (r-dose): Update to 3.18.3. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a03ed6453f..5bbb351ae4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7429,14 +7429,14 @@ to multiple hypothesis correction.") (define-public r-dose (package (name "r-dose") - (version "3.18.2") + (version "3.18.3") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "0kp6j42mpxrpd02cjrzqmrx3rvvpi90xiy4gc5km6ny3vxbhlaqw")))) + "09blmrgzxaknn263zf3zqc5yx27wjwznsr8lqsm118k4wpfxj504")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From a6f270b7afe707d2525d1b4790acc3921bc71f72 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 3 Nov 2021 11:37:22 +0000 Subject: gnu: r-enrichplot: Update to 1.12.3. * gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.12.3. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5bbb351ae4..8bf840d0f6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7464,14 +7464,14 @@ data.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.12.2") + (version "1.12.3") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "194sfmcnjfi3fvvfpljg1f80f44vvvxiij336b8z1dgzki6bqa3r")))) + "0a4v7ymy9jn66iw093jngzszkvr2mfzzlxp0h6nnvlbnbvqqzgm3")))) (build-system r-build-system) (propagated-inputs `(("r-cowplot" ,r-cowplot) -- cgit 1.4.1 From c00ca981a950c644830ac2f988c06485780a254e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 3 Nov 2021 11:37:22 +0000 Subject: gnu: r-motifstack: Update to 1.36.1. * gnu/packages/bioconductor.scm (r-motifstack): Update to 1.36.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8bf840d0f6..d1007cfdd5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8033,14 +8033,14 @@ Bioconductor.") (define-public r-motifstack (package (name "r-motifstack") - (version "1.36.0") + (version "1.36.1") (source (origin (method url-fetch) (uri (bioconductor-uri "motifStack" version)) (sha256 (base32 - "0yn348kmw7v46iym913ncx4yh5nxzmba8bdys52s12ldgjja53gp")))) + "140xclzgn5z64v5nm4kvj0qwvqb7ix91bbmimsfc6k1p0l8lwsvv")))) (properties `((upstream-name . "motifStack"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 81dad9f62d3df83e861723ce3c0245cf1d26021e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 3 Nov 2021 11:37:22 +0000 Subject: gnu: r-multidataset: Update to 1.20.2. * gnu/packages/bioconductor.scm (r-multidataset): Update to 1.20.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d1007cfdd5..ae41a34401 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9408,14 +9408,14 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.") (define-public r-multidataset (package (name "r-multidataset") - (version "1.20.0") + (version "1.20.2") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiDataSet" version)) (sha256 (base32 - "1hyk40xgmy50rqxwdvc64d3pgz5vsg8vmlj5cp5m0n5m0adxcdfj")))) + "06wcncz10jm54g0m9yk2314lg8x666p5r4zhi57sp2p50cj1lvnz")))) (properties `((upstream-name . "MultiDataSet"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From fdb9a02a68fb81f5a369b5859fe8286e0279b653 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 3 Nov 2021 11:37:22 +0000 Subject: gnu: r-s4vectors: Update to 0.30.2. * gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.30.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ae41a34401..914bf5ab09 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12380,13 +12380,13 @@ routines.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.30.1") + (version "0.30.2") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "103sw0fmmm4f3hprrsn7dwg0kmmr9mcmb46dcwwb6p5np0al2sfx")))) + "0n13j8fkiy8b071wvwwh3ip9cvq22f74hb1msx91mdab2xl47zxs")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) -- cgit 1.4.1 From 2f8a3af0b1988b59538fe3c6813aa4f0c12e3a28 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 21 Sep 2021 12:36:36 +0200 Subject: gnu: rust-rayon-core-1: Update to 1.9.1. * gnu/packages/crates-io.scm (rust-rayon-core-1): Update to 1.9.1. --- gnu/packages/crates-io.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index c76142bc58..3a681b6660 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -39133,14 +39133,14 @@ Rust.") (define-public rust-rayon-core-1 (package (name "rust-rayon-core") - (version "1.9.0") + (version "1.9.1") (source (origin (method url-fetch) (uri (crate-uri "rayon-core" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "0jpsi8zf66xyx4m5f329lpgiql8775vpm6zqm7zn5p11b6n4dcws")))) + (base32 "13kdcnqp2p1a5a3amamfjpnm7ay463vq4dfxy4rrh9shr3i210fp")))) (build-system cargo-build-system) (arguments ;; One of the tests attempts to overflow the stack, but the compiler has -- cgit 1.4.1 From a2b7abb99bd5396c59b404160c3bafa810be470a Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 21 Sep 2021 12:37:09 +0200 Subject: gnu: rust-rayon-1: Update to 1.5.1. * gnu/packages/crates-io.scm (rust-rayon-1): Update to 1.5.1. --- gnu/packages/crates-io.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 3a681b6660..05576ebfe8 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -39054,14 +39054,14 @@ accessors.") (define-public rust-rayon-1 (package (name "rust-rayon") - (version "1.5.0") + (version "1.5.1") (source (origin (method url-fetch) (uri (crate-uri "rayon" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "0x2n4zkrm6z3avdfh7zgcwx0wq6hx8332dx89v3j1p7s3448w3cb")))) + (base32 "143dl2453bazgk7rwjrickmyqd0ks3q69nfz8axcins19n0clsn0")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs -- cgit 1.4.1 From cc415fd880fea9059e6d0bd4c45ce143126d9f14 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 21 Sep 2021 12:38:20 +0200 Subject: gnu: Add rust-sysinfo-0.20. * gnu/packages/crates-io.scm (rust-sysinfo-0.20): New variable. --- gnu/packages/crates-io.scm | 35 ++++++++++++++++++++++++++++++----- 1 file changed, 30 insertions(+), 5 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 05576ebfe8..c13093d846 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -49637,10 +49637,10 @@ no_std compatible by default, only relying on alloc.") ("rust-errno" ,rust-errno-0.2) ("rust-libc" ,rust-libc-0.2)))))) -(define-public rust-sysinfo-0.18 +(define-public rust-sysinfo-0.20 (package (name "rust-sysinfo") - (version "0.18.2") + (version "0.20.3") (source (origin (method url-fetch) @@ -49648,15 +49648,14 @@ no_std compatible by default, only relying on alloc.") (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 - "0zd974yydc4yszxgx9hiqm5ah2rqnsgyq3qrl7raf90scpxaw16l")))) + (base32 "0ljf8cdn50g9vrg4h9qxv070n4zd83cv63g62007qs8d8n1pimwj")))) (build-system cargo-build-system) (arguments `(#:skip-build? #t + #:rust ,rust-1.54 #:cargo-inputs (("rust-cfg-if" ,rust-cfg-if-1) ("rust-core-foundation-sys" ,rust-core-foundation-sys-0.8) - ("rust-doc-comment" ,rust-doc-comment-0.3) ("rust-libc" ,rust-libc-0.2) ("rust-ntapi" ,rust-ntapi-0.3) ("rust-once-cell" ,rust-once-cell-1) @@ -49669,6 +49668,32 @@ no_std compatible by default, only relying on alloc.") processors, disks, components and networks.") (license license:expat))) +(define-public rust-sysinfo-0.18 + (package + (inherit rust-sysinfo-0.20) + (name "rust-sysinfo") + (version "0.18.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "sysinfo" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0zd974yydc4yszxgx9hiqm5ah2rqnsgyq3qrl7raf90scpxaw16l")))) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-cfg-if" ,rust-cfg-if-1) + ("rust-core-foundation-sys" ,rust-core-foundation-sys-0.8) + ("rust-doc-comment" ,rust-doc-comment-0.3) + ("rust-libc" ,rust-libc-0.2) + ("rust-ntapi" ,rust-ntapi-0.3) + ("rust-once-cell" ,rust-once-cell-1) + ("rust-rayon" ,rust-rayon-1) + ("rust-winapi" ,rust-winapi-0.3)))))) + (define-public rust-sysinfo-0.16 (package (inherit rust-sysinfo-0.18) -- cgit 1.4.1 From 64662ca9886f927660ce26674a24ad61c2985c25 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 16:18:26 +0200 Subject: gnu: Add rust-ego-tree-0.6. * gnu/packages/crates-io.scm (rust-ego-tree-0.6): New variable. --- gnu/packages/crates-io.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index c13093d846..0091b4967d 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -15346,6 +15346,24 @@ signing, and verification in pure Rust.") "Levenshtein edit distance between strings, a measure for similarity.") (license license:asl2.0))) +(define-public rust-ego-tree-0.6 + (package + (name "rust-ego-tree") + (version "0.6.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "ego-tree" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "149mkc6j7bx653s39rpnsnpl5dvd1rj18czcil57w54k868a8s1s")))) + (build-system cargo-build-system) + (arguments `(#:skip-build? #t)) + (home-page "https://github.com/programble/ego-tree") + (synopsis "Vec-backed ID-tree") + (description "Ego Tree provides a vec-backed ID-tree.") + (license license:isc))) + (define-public rust-either-1 (package (name "rust-either") -- cgit 1.4.1 From 3cafe8c198ce524131e2cf85e847c7a3c7730b33 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 16:19:30 +0200 Subject: gnu: Add rust-scraper-0.12. * gnu/packages/crates-io.scm (rust-scraper-0.12): New variable. --- gnu/packages/crates-io.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 0091b4967d..831022b553 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -43394,6 +43394,36 @@ with one of the implemented strategies.") (base32 "09sy9wbqp409pkwmqni40qmwa99ldqpl48pp95m1xw8sc19qy9cl")))))) +(define-public rust-scraper-0.12 + (package + (name "rust-scraper") + (version "0.12.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "scraper" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "04icx88wdrlz1qv0dz1zc0inlfq34ajwdpih854jw368j2kjmq28")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-cssparser" ,rust-cssparser-0.27) + ("rust-ego-tree" ,rust-ego-tree-0.6) + ("rust-getopts" ,rust-getopts-0.2) + ("rust-html5ever" ,rust-html5ever-0.25) + ("rust-matches" ,rust-matches-0.1) + ("rust-selectors" ,rust-selectors-0.22) + ("rust-smallvec" ,rust-smallvec-1) + ("rust-tendril" ,rust-tendril-0.4)))) + (home-page "https://github.com/programble/scraper") + (synopsis "HTML parsing and querying with CSS selectors") + (description + "Scraper provides an interface to Servo's html5ever and selectors crates, +for browser-grade parsing and querying.") + (license license:isc))) + (define-public rust-scratch-1 (package (name "rust-scratch") -- cgit 1.4.1 From 91301b5a511b19213b7c4a84474f6e2b8309cc4e Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 16:20:16 +0200 Subject: gnu: rust-strip-ansi-escapes-0.1: Update to 0.1.1. * gnu/packages/crates-io.scm (rust-strip-ansi-escapes-0.1): Update to 0.1.1. --- gnu/packages/crates-io.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 831022b553..bd7b1e894c 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -48266,19 +48266,19 @@ as defined in RFC 3454.") (define-public rust-strip-ansi-escapes-0.1 (package (name "rust-strip-ansi-escapes") - (version "0.1.0") + (version "0.1.1") (source (origin (method url-fetch) (uri (crate-uri "strip-ansi-escapes" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "1vmc6cwxsvp02b17b6x42mnnnn5vlc1dqbcqc2a71yms59p6fqwx")))) + (base32 "1n36ly9vxb1wr5q76i7995xr7c0pb1pc8g7a3a3n47vwrwwvn701")))) (build-system cargo-build-system) (arguments `(#:skip-build? #t #:cargo-inputs - (("rust-vte" ,rust-vte-0.3)))) + (("rust-vte" ,rust-vte-0.10)))) (home-page "https://github.com/luser/strip-ansi-escapes") (synopsis "Strip ANSI escape sequences from byte streams") (description -- cgit 1.4.1 From ea7246bb9fda697995a69ddac6061063e4a77b2a Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 16:22:28 +0200 Subject: gnu: Add rust-strength-reduce-0.2. * gnu/packages/crates-io.scm (rust-strength-reduce-0.2): New variable. --- gnu/packages/crates-io.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index bd7b1e894c..b60516f968 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -48095,6 +48095,30 @@ UTF-8.") "This package provides a streebog (GOST R 34.11-2012) hash function.") (license (list license:expat license:asl2.0)))) +(define-public rust-strength-reduce-0.2 + (package + (name "rust-strength-reduce") + (version "0.2.3") + (source + (origin + (method url-fetch) + (uri (crate-uri "strength_reduce" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0m12phq654mfxpmh2h5akqkag5ha6nlhjc2bp9jwarr5r1qjzzx3")))) + (build-system cargo-build-system) + (arguments `(#:skip-build? #t)) + (home-page "http://github.com/ejmahler/strength_reduce") + (synopsis "Faster integer division and modulus operations") + (description "Strength_reduce implements integer division and modulo via +@dfn{arithmetic strength reduction}. Modern processors can do multiplication +and shifts much faster than division, and arithmetic strength reduction is an +algorithm to transform divisions into multiplications and shifts. Compilers +already perform this optimization for divisors that are known at compile time; +this library enables this optimization for divisors that are only known at +runtime.") + (license (list license:expat license:asl2.0)))) + (define-public rust-string-0.2 (package (name "rust-string") -- cgit 1.4.1 From b6b132865d9fc6b8f1798a672f78d6eb746e2016 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 16:24:03 +0200 Subject: gnu: Add rust-streaming-iterator-0.1. * gnu/packages/crates-io.scm (rust-streaming-iterator-0.1): New variable. --- gnu/packages/crates-io.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index b60516f968..554c1bc47a 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -48044,6 +48044,29 @@ UTF-8.") (("rust-blobby" ,rust-blobby-0.1) ("rust-generic-array" ,rust-generic-array-0.13)))))) +(define-public rust-streaming-iterator-0.1 + (package + (name "rust-streaming-iterator") + (version "0.1.5") + (source + (origin + (method url-fetch) + (uri (crate-uri "streaming-iterator" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1xc1gyq137b020m29g85zdhbbdrksdmhf3dq4ri4fjlrfz0kacih")))) + (build-system cargo-build-system) + (arguments `(#:skip-build? #t)) + (home-page "https://github.com/sfackler/streaming-iterator") + (synopsis "Streaming iterators") + (description "The iterator APIs in the Rust standard library do not allow +elements to be yielded which borrow from the iterator itself. That means, for +example, that the @code{std::io::Lines} iterator must allocate a new +@code{String} for each line rather than reusing an internal buffer. The +@code{StreamingIterator} trait instead provides access to elements being +iterated over only by reference rather than by value.") + (license (list license:expat license:asl2.0)))) + (define-public rust-streaming-stats-0.2 (package (name "rust-streaming-stats") -- cgit 1.4.1 From da0a5bbb19c38ef9a71021c28f732c191b9e357a Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 16:25:00 +0200 Subject: gnu: Add rust-integer-encoding-3. * gnu/packages/crates-io.scm (rust-integer-encoding-3): New variable. (rust-integer-encoding-1): Inherit from above. --- gnu/packages/crates-io.scm | 27 +++++++++++++++++++++++---- 1 file changed, 23 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 554c1bc47a..87e29c038d 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -23635,24 +23635,24 @@ data efficiently.") that works on WASM too.") (license license:bsd-3))) -(define-public rust-integer-encoding-1 +(define-public rust-integer-encoding-3 (package (name "rust-integer-encoding") - (version "1.2.2") + (version "3.0.2") (source (origin (method url-fetch) (uri (crate-uri "integer-encoding" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "1c032xhif5d6a8nc4cak60g5ylwd6p9569122m5hm67brx2l5yhb")))) + (base32 "1f0mk7d694g2sz4my5zh7i5w4kijx5y16x6dip7fv0pazx013hch")))) (build-system cargo-build-system) (arguments `(#:skip-build? #t #:cargo-inputs (("rust-async-trait" ,rust-async-trait-0.1) ("rust-futures-util" ,rust-futures-util-0.3) - ("rust-tokio" ,rust-tokio-0.2)))) + ("rust-tokio" ,rust-tokio-1)))) (home-page "https://github.com/dermesser/integer-encoding-rs") (synopsis "Encoding and decoding integers to and from bytestrings") (description @@ -23660,6 +23660,25 @@ that works on WASM too.") bytestring representations.") (license license:expat))) +(define-public rust-integer-encoding-1 + (package + (inherit rust-integer-encoding-3) + (name "rust-integer-encoding") + (version "1.2.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "integer-encoding" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1c032xhif5d6a8nc4cak60g5ylwd6p9569122m5hm67brx2l5yhb")))) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-async-trait" ,rust-async-trait-0.1) + ("rust-futures-util" ,rust-futures-util-0.3) + ("rust-tokio" ,rust-tokio-0.2)))))) + (define-public rust-interpolate-name-0.2 (package (name "rust-interpolate-name") -- cgit 1.4.1 From ffe982b18ba1cfd067d4850e48d073cd6a9d1e9d Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 16:27:41 +0200 Subject: gnu: rust-bitpacking-0.8: Update to 0.8.4. * gnu/packages/crates-io.scm (rust-bitpacking-0.8): Update to 0.8.4. --- gnu/packages/crates-io.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 87e29c038d..14085f69f8 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -5454,6 +5454,27 @@ behave like a set of bitflags.") declaring and working with fixed size bitmaps in Rust.") (license license:mpl2.0))) +(define-public rust-bitpacking-0.8 + (package + (name "rust-bitpacking") + (version "0.8.4") + (source + (origin + (method url-fetch) + (uri (crate-uri "bitpacking" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1mw2xbpkw9zhfq5lir6bgkalhhfqb5p7xwx5yimc0ry1ffnd5ix8")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t #:cargo-inputs (("rust-crunchy" ,rust-crunchy-0.2)))) + (home-page "https://crates.io/crates/bitpacking") + (synopsis "Fast integer compression/decompression via SIMD bit-packing") + (description + "This crate provides fast integer compression and decompression via SIMD +bit-packing. It is a port of simdcomp C library to Rust.") + (license license:expat))) + (define-public rust-bitreader-0.3 (package (name "rust-bitreader") -- cgit 1.4.1 From bd48b7d8fa38421a9eecf151d6540e3eddcd1cbe Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 16:30:30 +0200 Subject: gnu: rust-async-stream-impl-0.3: Update to 0.3.2. * gnu/packages/crates-io.scm (rust-async-stream-impl-0.3): Update to 0.3.2. --- gnu/packages/crates-io.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 14085f69f8..fd97fd5cbc 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -3679,14 +3679,14 @@ notation.") (define-public rust-async-stream-impl-0.3 (package (name "rust-async-stream-impl") - (version "0.3.0") + (version "0.3.2") (source (origin (method url-fetch) (uri (crate-uri "async-stream-impl" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "0w0aif9aw103b5wrm1svkqdh7aaihjywa21819d8m3lzzj78nm53")))) + (base32 "024k57iwmmhzvbzacxlkssh45cqlnb8xjlvlsp60jm6fsb4di3k4")))) (build-system cargo-build-system) (arguments `(#:cargo-test-flags '("--release" "--" -- cgit 1.4.1 From 4dca103962694ee5141c583fbd52e26cc2b3f275 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 16:51:15 +0200 Subject: gnu: rust-async-stream-0.3: Update to 0.3.2. * gnu/packages/crates-io.scm (rust-async-stream-0.3): Update to 0.3.2. --- gnu/packages/crates-io.scm | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index fd97fd5cbc..aea871e1d8 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -3651,23 +3651,25 @@ interfaces you are used to, but in an async version and ready for Rust's (define-public rust-async-stream-0.3 (package (name "rust-async-stream") - (version "0.3.0") + (version "0.3.2") (source (origin (method url-fetch) (uri (crate-uri "async-stream" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "0p19qn5igblb86d35lda72q8vimk2iw8hk7r07wjj5y0rdqdyw1n")))) + (base32 "0986b72jksg4lndw76py9glry3snc29bbqrna874wl5jwgkp84qp")))) (build-system cargo-build-system) (arguments - `(#:cargo-inputs + `(#:cargo-test-flags '("--release" "--" + "--skip=test") + #:cargo-inputs (("rust-async-stream-impl" ,rust-async-stream-impl-0.3) ("rust-futures-core" ,rust-futures-core-0.3)) #:cargo-development-inputs (("rust-futures-util" ,rust-futures-util-0.3) - ("rust-tokio" ,rust-tokio-0.2) - ("rust-tokio-test" ,rust-tokio-test-0.2) + ("rust-tokio" ,rust-tokio-1) + ("rust-tokio-test" ,rust-tokio-test-0.4) ("rust-trybuild" ,rust-trybuild-1)))) (home-page "https://github.com/tokio-rs/async-stream") (synopsis "Asynchronous streams using async & await notation") @@ -3699,7 +3701,7 @@ notation.") #:cargo-development-inputs (("rust-futures-core" ,rust-futures-core-0.3) ("rust-futures-util" ,rust-futures-util-0.3) - ("rust-tokio" ,rust-tokio-0.2)))) + ("rust-tokio" ,rust-tokio-1)))) (home-page "https://github.com/tokio-rs/async-stream") (synopsis "Proc macros for async-stream crate") (description -- cgit 1.4.1 From 1ab8cdedef2ffb39039279d9effd608df931417b Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 16:52:14 +0200 Subject: gnu: Add rust-hash-hasher-2. * gnu/packages/crates-io.scm (rust-hash-hasher-2): New variable. --- gnu/packages/crates-io.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index aea871e1d8..40896056a4 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -21146,6 +21146,26 @@ the template engine that renders the official Rust website") "This package provides a Rust implementation of VG handle graph.") (license license:expat))) +(define-public rust-hash-hasher-2 + (package + (name "rust-hash-hasher") + (version "2.0.3") + (source + (origin + (method url-fetch) + (uri (crate-uri "hash_hasher" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "034cd4m3znwff3cd1i54c40944y999jz086d70rwpl0jfl01swkl")))) + (build-system cargo-build-system) + (arguments `(#:skip-build? #t)) + (home-page "https://github.com/Fraser999/Hash-Hasher.git") + (synopsis "Hasher designed to work with already-hashed or hash-like data") + (description + "This package provides a hasher which is designed to work with +already-hashed or hash-like data.") + (license (list license:asl2.0 license:expat)))) + (define-public rust-hash32-0.1 (package (name "rust-hash32") -- cgit 1.4.1 From 035b9cff0ce5d21562d628fd0dee8e2cd6279745 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 17:39:47 +0200 Subject: gnu: Add rust-strum-macros-0.21. * gnu/packages/crates-io.scm (rust-strum-macros-0.21): New variable. (rust-strum-macros-0.20): Inherit from above. --- gnu/packages/crates-io.scm | 26 +++++++++++++++++++++++--- 1 file changed, 23 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 40896056a4..92f3b7db23 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -48708,17 +48708,17 @@ easier in Rust.") `(#:cargo-inputs (("rust-strum-macros" ,rust-strum-macros-0.18)))))) -(define-public rust-strum-macros-0.20 +(define-public rust-strum-macros-0.21 (package (name "rust-strum-macros") - (version "0.20.1") + (version "0.21.1") (source (origin (method url-fetch) (uri (crate-uri "strum_macros" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "0j9ikvxlqzr667ghc045qkpwprjgcfmzgagln7maw4jigawcd2zf")))) + (base32 "1v55b1in7dn07s6vxr8dajqpvxkxjbfq6qamnjgcbnq9x3pawsnh")))) (build-system cargo-build-system) (arguments `(#:skip-build? #t @@ -48733,6 +48733,26 @@ easier in Rust.") "This crate provides helpful macros for working with enums and strings.") (license license:expat))) +(define-public rust-strum-macros-0.20 + (package + (inherit rust-strum-macros-0.21) + (name "rust-strum-macros") + (version "0.20.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "strum_macros" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0j9ikvxlqzr667ghc045qkpwprjgcfmzgagln7maw4jigawcd2zf")))) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-heck" ,rust-heck-0.3) + ("rust-proc-macro2" ,rust-proc-macro2-1) + ("rust-quote" ,rust-quote-1) + ("rust-syn" ,rust-syn-1)))))) + (define-public rust-strum-macros-0.19 (package (inherit rust-strum-macros-0.20) -- cgit 1.4.1 From daaa7c4c53aaf1689265c592e98d989e8c4f89a0 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 17:40:31 +0200 Subject: gnu: Add rust-strum-0.21. * gnu/packages/crates-io.scm (rust-strum-0.21): New variable. (rust-strum-0.20): Inherit from above. --- gnu/packages/crates-io.scm | 25 +++++++++++++++++++++---- 1 file changed, 21 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 92f3b7db23..672a840915 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -48651,22 +48651,22 @@ struct.") "Parse command line argument by defining a struct, derive crate.") (license (list license:asl2.0 license:expat)))) -(define-public rust-strum-0.20 +(define-public rust-strum-0.21 (package (name "rust-strum") - (version "0.20.0") + (version "0.21.0") (source (origin (method url-fetch) (uri (crate-uri "strum" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "0p5cslmdnz261kiwmm4h7qsmv9bh83r0f9lq6f2z2mxsnl4wa63k")))) + (base32 "1qnd2by1zrwgx7li0hmwy7jbzjwz1ky697qjg85nga8zzny6py5a")))) (build-system cargo-build-system) (arguments `(#:skip-build? #t #:cargo-inputs - (("rust-strum-macros" ,rust-strum-macros-0.20)))) + (("rust-strum-macros" ,rust-strum-macros-0.21)))) (home-page "https://github.com/Peternator7/strum") (synopsis "Set of traits for working with enums and strings") (description @@ -48674,6 +48674,23 @@ struct.") easier in Rust.") (license license:expat))) +(define-public rust-strum-0.20 + (package + (inherit rust-strum-0.21) + (name "rust-strum") + (version "0.20.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "strum" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0p5cslmdnz261kiwmm4h7qsmv9bh83r0f9lq6f2z2mxsnl4wa63k")))) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-strum-macros" ,rust-strum-macros-0.20)))))) + (define-public rust-strum-0.19 (package (inherit rust-strum-0.20) -- cgit 1.4.1 From e651523b3f79554064a76a35f15ef498d2ab9390 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 17:41:41 +0200 Subject: gnu: Add rust-crossterm-winapi-0.8. * gnu/packages/crates-io.scm (rust-crossterm-winapi-0.8): New variable. (rust-crossterm-winapi-0.7): Inherit from above. --- gnu/packages/crates-io.scm | 26 +++++++++++++++++++++----- 1 file changed, 21 insertions(+), 5 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 672a840915..25ddb02e42 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -11500,22 +11500,21 @@ terminals.") ("rust-serde" ,rust-serde-1) ("rust-winapi" ,rust-winapi-0.3)))))) -(define-public rust-crossterm-winapi-0.7 +(define-public rust-crossterm-winapi-0.8 (package (name "rust-crossterm-winapi") - (version "0.7.0") + (version "0.8.0") (source (origin (method url-fetch) (uri (crate-uri "crossterm_winapi" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "1fa047zz228qyqbcjdss64j0n01p4adr29yh9w24lgjdrr59da0d")))) + (base32 "01q57jwnlicqxa2igg5nig3916kf5w6sqgbxk40q6hr2frh6cs9s")))) (build-system cargo-build-system) (arguments `(#:skip-build? #t - #:cargo-inputs - (("rust-winapi" ,rust-winapi-0.3)))) + #:cargo-inputs (("rust-winapi" ,rust-winapi-0.3)))) (home-page "https://github.com/crossterm-rs/crossterm-winapi") (synopsis "Basic simple abstractions around common WinAPI calls") (description @@ -11523,6 +11522,23 @@ terminals.") abstractions around common WinAPI calls.") (license license:expat))) +(define-public rust-crossterm-winapi-0.7 + (package + (inherit rust-crossterm-winapi-0.8) + (name "rust-crossterm-winapi") + (version "0.7.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "crossterm_winapi" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1fa047zz228qyqbcjdss64j0n01p4adr29yh9w24lgjdrr59da0d")))) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-winapi" ,rust-winapi-0.3)))))) + (define-public rust-crossterm-winapi-0.6 (package (inherit rust-crossterm-winapi-0.7) -- cgit 1.4.1 From d48c95d77086c6ebba5c715e5f82074cf161ddc4 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 17:42:51 +0200 Subject: gnu: rust-signal-hook-registry-1: Update to 1.4.0. * gnu/packages/crates-io.scm (rust-signal-hook-registry-1): Update to 1.4.0. --- gnu/packages/crates-io.scm | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 25ddb02e42..0a02a25c1d 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -46266,16 +46266,14 @@ words, like Python's shlex.") (define-public rust-signal-hook-registry-1 (package (name "rust-signal-hook-registry") - (version "1.3.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (crate-uri "signal-hook-registry" version)) - (file-name - (string-append name "-" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 - "19hirq0h33jjyh505s8hf9q5dq0ky80ygivkl3vshjv0y7zd1w8n")))) + (base32 "1c2mhijg54y6c1zi4630yki1vpq3z96ljfnsrdy0rb64ilr767p5")))) (build-system cargo-build-system) (arguments `(#:skip-build? #t -- cgit 1.4.1 From d46c6b74eda8f00dbcdd5d74b1952d88dd0c5cee Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 17:43:31 +0200 Subject: gnu: rust-signal-hook-0.3: Update to 0.3.10. * gnu/packages/crates-io.scm (rust-signal-hook-0.3): Update to 0.3.10. --- gnu/packages/crates-io.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 0a02a25c1d..1a4d68b18c 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -46217,14 +46217,14 @@ words, like Python's shlex.") (define-public rust-signal-hook-0.3 (package (name "rust-signal-hook") - (version "0.3.4") + (version "0.3.10") (source (origin (method url-fetch) (uri (crate-uri "signal-hook" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "0h628smm9y22qi3szpkg3xpj31hyvs4ps29nf8cnfvy6w0zmw3vq")))) + (base32 "1lgg8rwyz97pqkpg4ii7iswvs5mx8sgg2pl2ahlil9vyfcfqk64w")))) (build-system cargo-build-system) (arguments `(#:skip-build? #t -- cgit 1.4.1 From 5daad8fae6300b3786b76a7425ab054e5ff0969e Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 17:44:37 +0200 Subject: gnu: rust-signal-hook-mio-0.2: Update to 0.2.1. * gnu/packages/crates-io.scm (rust-signal-hook-mio-0.2): Update to 0.2.1. --- gnu/packages/crates-io.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 1a4d68b18c..f00bc5cbbf 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -46263,6 +46263,31 @@ words, like Python's shlex.") (("rust-tokio" ,rust-tokio-0.1) ("rust-version-sync" ,rust-version-sync-0.8)))))) +(define-public rust-signal-hook-mio-0.2 + (package + (name "rust-signal-hook-mio") + (version "0.2.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "signal-hook-mio" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1m3yc37dxdq4ym0x7i2b9aqfnlhivwm7mvls0yzcbwn4y5kmiz99")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-libc" ,rust-libc-0.2) + ("rust-mio" ,rust-mio-0.7) + ("rust-mio" ,rust-mio-0.6) + ("rust-mio-uds" ,rust-mio-uds-0.6) + ("rust-signal-hook" ,rust-signal-hook-0.3)))) + (home-page "https://github.com/vorner/signal-hook") + (synopsis "MIO support for signal-hook") + (description "This crate provides MIO support for signal-hook.") + (license (list license:asl2.0 license:expat)))) + (define-public rust-signal-hook-registry-1 (package (name "rust-signal-hook-registry") -- cgit 1.4.1 From 7e12354cd1d1b787c542c06526f0d5f8e479e962 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 17:45:21 +0200 Subject: gnu: Add rust-crossterm-0.20. * gnu/packages/crates-io.scm (rust-crossterm-0.20): New variable. (rust-crossterm-0.19): Inherit from above. --- gnu/packages/crates-io.scm | 38 ++++++++++++++++++++++++++++++++------ 1 file changed, 32 insertions(+), 6 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index f00bc5cbbf..7c05a17620 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -11421,30 +11421,30 @@ rasterizing glyphs, using native font engines whenever possible.") ("rust-servo-fontconfig" ,rust-servo-fontconfig-0.5) ("rust-winapi" ,rust-winapi-0.3)))))) -(define-public rust-crossterm-0.19 +(define-public rust-crossterm-0.20 (package (name "rust-crossterm") - (version "0.19.0") + (version "0.20.0") (source (origin (method url-fetch) (uri (crate-uri "crossterm" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "1348lqf8vy3lb2s5icsl3rxs4a4vrpfw5z2j6lplnhnz600w2dkw")))) + (base32 "0z8zkk2mfiirbr3slfv564n685yiahr2aj3gdk6k3qymkmmdxsy0")))) (build-system cargo-build-system) (arguments `(#:skip-build? #t #:cargo-inputs (("rust-bitflags" ,rust-bitflags-1) - ("rust-crossterm-winapi" ,rust-crossterm-winapi-0.7) + ("rust-crossterm-winapi" ,rust-crossterm-winapi-0.8) ("rust-futures-core" ,rust-futures-core-0.3) - ("rust-lazy-static" ,rust-lazy-static-1) ("rust-libc" ,rust-libc-0.2) ("rust-mio" ,rust-mio-0.7) ("rust-parking-lot" ,rust-parking-lot-0.11) ("rust-serde" ,rust-serde-1) - ("rust-signal-hook" ,rust-signal-hook-0.1) + ("rust-signal-hook" ,rust-signal-hook-0.3) + ("rust-signal-hook-mio" ,rust-signal-hook-mio-0.2) ("rust-winapi" ,rust-winapi-0.3)))) (home-page "https://github.com/crossterm-rs/crossterm") (synopsis "Crossplatform terminal library for manipulating terminals") @@ -11453,6 +11453,32 @@ rasterizing glyphs, using native font engines whenever possible.") terminals.") (license license:expat))) +(define-public rust-crossterm-0.19 + (package + (inherit rust-crossterm-0.20) + (name "rust-crossterm") + (version "0.19.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "crossterm" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1348lqf8vy3lb2s5icsl3rxs4a4vrpfw5z2j6lplnhnz600w2dkw")))) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-bitflags" ,rust-bitflags-1) + ("rust-crossterm-winapi" ,rust-crossterm-winapi-0.7) + ("rust-futures-core" ,rust-futures-core-0.3) + ("rust-lazy-static" ,rust-lazy-static-1) + ("rust-libc" ,rust-libc-0.2) + ("rust-mio" ,rust-mio-0.7) + ("rust-parking-lot" ,rust-parking-lot-0.11) + ("rust-serde" ,rust-serde-1) + ("rust-signal-hook" ,rust-signal-hook-0.1) + ("rust-winapi" ,rust-winapi-0.3)))))) + (define-public rust-crossterm-0.18 (package (inherit rust-crossterm-0.19) -- cgit 1.4.1 From a21bb7f6f7f9ad1b09a0b3da06f511914accb89b Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 17:46:12 +0200 Subject: gnu: Add rust-comfy-table-4. * gnu/packages/crates-io.scm (rust-comfy-table-4): New variable. (rust-comfy-table-1): Inherit from above. --- gnu/packages/crates-io.scm | 32 ++++++++++++++++++++++++++------ 1 file changed, 26 insertions(+), 6 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 7c05a17620..33f33317f1 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -9424,24 +9424,25 @@ combinator.") and 1.0.") (license (list license:expat license:asl2.0)))) -(define-public rust-comfy-table-1 +(define-public rust-comfy-table-4 (package (name "rust-comfy-table") - (version "1.6.0") + (version "4.1.1") (source (origin (method url-fetch) (uri (crate-uri "comfy-table" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "1y6lc8h2lyyrrrdc36fz7brwyjz5l9w4nld4qx9mlacfibm8i92j")))) + (base32 "1wzk894p2s725cpdip5968ydb50zczsl34040j6zs8klhqz5ms8i")))) (build-system cargo-build-system) (arguments `(#:skip-build? #t #:cargo-inputs - (("rust-crossterm" ,rust-crossterm-0.19) - ("rust-strum" ,rust-strum-0.20) - ("rust-strum-macros" ,rust-strum-macros-0.20)))) + (("rust-crossterm" ,rust-crossterm-0.20) + ("rust-strum" ,rust-strum-0.21) + ("rust-strum-macros" ,rust-strum-macros-0.21) + ("rust-unicode-width" ,rust-unicode-width-0.1)))) (home-page "https://github.com/nukesor/comfy-table") (synopsis "Library for building tables with automatic content wrapping") (description @@ -9449,6 +9450,25 @@ and 1.0.") wrapping.") (license license:expat))) +(define-public rust-comfy-table-1 + (package + (inherit rust-comfy-table-4) + (name "rust-comfy-table") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "comfy-table" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1y6lc8h2lyyrrrdc36fz7brwyjz5l9w4nld4qx9mlacfibm8i92j")))) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-crossterm" ,rust-crossterm-0.19) + ("rust-strum" ,rust-strum-0.20) + ("rust-strum-macros" ,rust-strum-macros-0.20)))))) + (define-public rust-commoncrypto-sys-0.2 (package (name "rust-commoncrypto-sys") -- cgit 1.4.1 From 01d52c1876f24b061371666fa27335d89f920845 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 21:36:35 +0200 Subject: gnu: Add rust-lexical-util-0.8. * gnu/packages/crates-io.scm (rust-lexical-util-0.8): New variable. --- gnu/packages/crates-io.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 33f33317f1..84bec551aa 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -25373,6 +25373,27 @@ sending emails from Rust applications.") ("rust-quickcheck" ,rust-quickcheck-0.8) ("rust-rustc-version" ,rust-rustc-version-0.2)))))) +(define-public rust-lexical-util-0.8 + (package + (name "rust-lexical-util") + (version "0.8.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "lexical-util" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "14g224mm2li0q6jnnqh92dzx3zjyflji3i8dz4xf6vp1mb66kxkg")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-static-assertions" ,rust-static-assertions-1)))) + (home-page "https://github.com/Alexhuszagh/rust-lexical") + (synopsis "Shared utilities for lexical crate") + (description "This package provides shared utilities for lexical crate.") + (license (list license:expat license:asl2.0)))) + (define-public rust-lexical-5 (package (name "rust-lexical") -- cgit 1.4.1 From 5a6d510d3e0685f921148ead4792b06f39b5cf52 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 21:37:24 +0200 Subject: gnu: Add rust-lexical-parse-integer-0.8. * gnu/packages/crates-io.scm (rust-lexical-parse-integer-0.8): New variable. --- gnu/packages/crates-io.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 84bec551aa..b24a80424c 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -25373,6 +25373,29 @@ sending emails from Rust applications.") ("rust-quickcheck" ,rust-quickcheck-0.8) ("rust-rustc-version" ,rust-rustc-version-0.2)))))) +(define-public rust-lexical-parse-integer-0.8 + (package + (name "rust-lexical-parse-integer") + (version "0.8.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "lexical-parse-integer" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1b2kxprq3636x3j1qy68202q7yzsmq5c7h9w7m7zrh4cvanjpjgj")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-lexical-util" ,rust-lexical-util-0.8) + ("rust-static-assertions" ,rust-static-assertions-1)))) + (home-page "https://github.com/Alexhuszagh/rust-lexical") + (synopsis "Efficient parsing of integers from strings") + (description + "This crate provides efficient parsing of integers from strings.") + (license (list license:expat license:asl2.0)))) + (define-public rust-lexical-util-0.8 (package (name "rust-lexical-util") -- cgit 1.4.1 From e18404703ba33a81fa19ee7137fb81eb7a602020 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 21:38:01 +0200 Subject: gnu: Add rust-lexical-write-integer-0.8. * gnu/packages/crates-io.scm (rust-lexical-write-integer-0.8): New variable. --- gnu/packages/crates-io.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index b24a80424c..f2b4b8558d 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -25417,6 +25417,29 @@ sending emails from Rust applications.") (description "This package provides shared utilities for lexical crate.") (license (list license:expat license:asl2.0)))) +(define-public rust-lexical-write-integer-0.8 + (package + (name "rust-lexical-write-integer") + (version "0.8.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "lexical-write-integer" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1vsn3zg2hyqnyapwmzb2aw0w5f53ad6s6n46xyazsh0f5r4mdsgc")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-lexical-util" ,rust-lexical-util-0.8) + ("rust-static-assertions" ,rust-static-assertions-1)))) + (home-page "https://github.com/Alexhuszagh/rust-lexical") + (synopsis "Efficient formatting of integers to strings") + (description + "This crate provides efficient formatting of integers to strings.") + (license (list license:expat license:asl2.0)))) + (define-public rust-lexical-5 (package (name "rust-lexical") -- cgit 1.4.1 From 8608e1e1b411ebd4f4b1101a6e5da5fcaa279643 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 21:38:28 +0200 Subject: gnu: Add rust-lexical-write-float-0.8. * gnu/packages/crates-io.scm (rust-lexical-write-float-0.8): New variable. --- gnu/packages/crates-io.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index f2b4b8558d..ea0e3ee393 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -25417,6 +25417,30 @@ sending emails from Rust applications.") (description "This package provides shared utilities for lexical crate.") (license (list license:expat license:asl2.0)))) +(define-public rust-lexical-write-float-0.8 + (package + (name "rust-lexical-write-float") + (version "0.8.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "lexical-write-float" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0xn5dpdmld2nvj7jvz3xrvjjbrnsh4jhymjimax7labvija8clcb")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-lexical-util" ,rust-lexical-util-0.8) + ("rust-lexical-write-integer" ,rust-lexical-write-integer-0.8) + ("rust-static-assertions" ,rust-static-assertions-1)))) + (home-page "https://github.com/Alexhuszagh/rust-lexical") + (synopsis "Efficient formatting of floats to strings") + (description + "This crate provides efficient formatting of floats to strings.") + (license (list license:expat license:asl2.0)))) + (define-public rust-lexical-write-integer-0.8 (package (name "rust-lexical-write-integer") -- cgit 1.4.1 From 6393bf60272c1f34b2cd6a9172aac27af37d3cdf Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 21:38:59 +0200 Subject: gnu: Add rust-lexical-parse-float-0.8. * gnu/packages/crates-io.scm (rust-lexical-parse-float-0.8): New variable. --- gnu/packages/crates-io.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index ea0e3ee393..2062da7970 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -25373,6 +25373,30 @@ sending emails from Rust applications.") ("rust-quickcheck" ,rust-quickcheck-0.8) ("rust-rustc-version" ,rust-rustc-version-0.2)))))) +(define-public rust-lexical-parse-float-0.8 + (package + (name "rust-lexical-parse-float") + (version "0.8.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "lexical-parse-float" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "03mzjx8k2jzv2vbl1xb589p9zfs5i2m23vcmm6fjsxps0k86dl5l")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-lexical-parse-integer" ,rust-lexical-parse-integer-0.8) + ("rust-lexical-util" ,rust-lexical-util-0.8) + ("rust-static-assertions" ,rust-static-assertions-1)))) + (home-page "https://github.com/Alexhuszagh/rust-lexical") + (synopsis "Efficient parsing of floats from strings") + (description + "This crate provides efficient parsing of floats from strings.") + (license (list license:expat license:asl2.0)))) + (define-public rust-lexical-parse-integer-0.8 (package (name "rust-lexical-parse-integer") -- cgit 1.4.1 From 2eb523a3894e01b83397ff7426b3df0aee3c8a0e Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 21:40:20 +0200 Subject: gnu: Add rust-lexical-core-0.8. * gnu/packages/crates-io.scm (rust-lexical-core-0.8): New variable. (rust-lexical-core-0.7): Inherit from above. --- gnu/packages/crates-io.scm | 38 +++++++++++++++++++++++++++++--------- 1 file changed, 29 insertions(+), 9 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 2062da7970..df08cd80b3 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -25311,8 +25311,36 @@ requires non-const function calls to be computed.") sending emails from Rust applications.") (license license:expat))) +(define-public rust-lexical-core-0.8 + (package + (name "rust-lexical-core") + (version "0.8.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "lexical-core" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1152ll9xa7v4jz2mjvz0048gy32yg39mzgjaps89h0any7c2cfba")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-lexical-parse-float" ,rust-lexical-parse-float-0.8) + ("rust-lexical-parse-integer" ,rust-lexical-parse-integer-0.8) + ("rust-lexical-util" ,rust-lexical-util-0.8) + ("rust-lexical-write-float" ,rust-lexical-write-float-0.8) + ("rust-lexical-write-integer" ,rust-lexical-write-integer-0.8)))) + (home-page + "https://github.com/Alexhuszagh/rust-lexical/tree/master/lexical-core") + (synopsis "Lexical, to- and from-string conversion routines") + (description + "This crate provides lexical, to- and from-string conversion routines.") + (license (list license:expat license:asl2.0)))) + (define-public rust-lexical-core-0.7 (package + (inherit rust-lexical-core-0.8) (name "rust-lexical-core") (version "0.7.6") (source @@ -25323,7 +25351,6 @@ sending emails from Rust applications.") (string-append name "-" version ".tar.gz")) (sha256 (base32 "1zjzab1fnaw4kj6ixyrskp4dyz761gdcab07m4bkvlk1l4mcc1v6")))) - (build-system cargo-build-system) (arguments `(#:cargo-inputs (("rust-arrayvec" ,rust-arrayvec-0.5) @@ -25336,14 +25363,7 @@ sending emails from Rust applications.") #:cargo-development-inputs (("rust-approx" ,rust-approx-0.4) ("rust-proptest" ,rust-proptest-0.10) - ("rust-quickcheck" ,rust-quickcheck-1)))) - (home-page - "https://github.com/Alexhuszagh/rust-lexical/tree/master/lexical-core") - (synopsis - "Lexical, to- and from-string conversion routines") - (description - "Lexical, to- and from-string conversion routines.") - (license (list license:expat license:asl2.0)))) + ("rust-quickcheck" ,rust-quickcheck-1)))))) (define-public rust-lexical-core-0.4 (package -- cgit 1.4.1 From fc9082e4e571c165a010806948275096a902a914 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 21:42:09 +0200 Subject: gnu: Add rust-lexical-6. * gnu/packages/crates-io.scm (rust-lexical-6): New variable. (rust-lexical-5): Inherit from above. --- gnu/packages/crates-io.scm | 34 ++++++++++++++++++++++++++-------- 1 file changed, 26 insertions(+), 8 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index df08cd80b3..19f35a2e45 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -25508,8 +25508,33 @@ sending emails from Rust applications.") "This crate provides efficient formatting of integers to strings.") (license (list license:expat license:asl2.0)))) +(define-public rust-lexical-6 + (package + (name "rust-lexical") + (version "6.0.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "lexical" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1y8v2s8g2hjinwf5hbm1ncbazw9q4qbp111q2mwacq6hi0grhkn3")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-lexical-core" ,rust-lexical-core-0.8)))) + (home-page "https://github.com/Alexhuszagh/rust-lexical") + (synopsis "Lexical, to- and from-string conversion routines") + (description + "Lexical is high-performance numeric conversion routines for use in +a no_std environment. This does not depend on any standard library features, +nor a system allocator.") + (license (list license:expat license:asl2.0)))) + (define-public rust-lexical-5 (package + (inherit rust-lexical-6) (name "rust-lexical") (version "5.2.2") (source @@ -25519,7 +25544,6 @@ sending emails from Rust applications.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 "1r8lsi523h53kbb99xgv31jabwhcp4rzqd4hfazfhcjffh5aj17l")))) - (build-system cargo-build-system) (arguments `(#:skip-build? #t #:cargo-inputs @@ -25528,13 +25552,7 @@ sending emails from Rust applications.") ("rust-rand" ,rust-rand-0.4) ("rust-serde" ,rust-serde-1) ("rust-serde-derive" ,rust-serde-derive-1) - ("rust-toml" ,rust-toml-0.5)))) - (home-page "https://github.com/Alexhuszagh/rust-lexical") - (synopsis "Lexical, to- and from-string conversion routines") - (description - "Lexical provides routines to convert numbers to and from decimal -strings.") - (license (list license:expat license:asl2.0)))) + ("rust-toml" ,rust-toml-0.5)))))) (define-public rust-libc-0.2 (package -- cgit 1.4.1 From 62f37580b923485c149e58320ddd7d8830b52536 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 21:43:32 +0200 Subject: gnu: Add rust-parquet-format-async-temp-0.2. * gnu/packages/crates-io.scm (rust-parquet-format-async-temp-0.2): New variable. --- gnu/packages/crates-io.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 19f35a2e45..401e4b27be 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -33985,6 +33985,33 @@ synchronization primitives.") file and the generated @file{.rs} file.") (license license:asl2.0))) +(define-public rust-parquet-format-async-temp-0.2 + (package + (name "rust-parquet-format-async-temp") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "parquet-format-async-temp" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0i7mn4x64d8g6d046y9kpb55dz8v0z67cz7lhgncxs9zr3ww5aq3")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-async-trait" ,rust-async-trait-0.1) + ("rust-byteorder" ,rust-byteorder-1) + ("rust-futures" ,rust-futures-0.3) + ("rust-integer-encoding" ,rust-integer-encoding-3) + ("rust-ordered-float" ,rust-ordered-float-1)))) + (home-page "https://github.com/sunchao/parquet-format-rs") + (synopsis "Temporary crate containing thrift library + parquet definitions") + (description + "This is a temporary crate containing thrift library and parquet +definitions compiled to support read+write async.") + (license license:asl2.0))) + (define-public rust-parse-zoneinfo-0.3 (package (name "rust-parse-zoneinfo") -- cgit 1.4.1 From b38d777ad04ffd31cf0621d38334838d3e57230e Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 21:45:33 +0200 Subject: gnu: Add rust-parquet2-0.4. * gnu/packages/crates-io.scm (rust-parquet2-0.4): New variable. --- gnu/packages/crates-io.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 401e4b27be..f26f672f84 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -34012,6 +34012,38 @@ file and the generated @file{.rs} file.") definitions compiled to support read+write async.") (license license:asl2.0))) +(define-public rust-parquet2-0.4 + (package + (name "rust-parquet2") + (version "0.4.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "parquet2" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1rsmrjy0r8q56gygycc5j0kgdbvrazh6xg6z8vcdyhn8r1v8yxbk")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-async-stream" ,rust-async-stream-0.3) + ("rust-bitpacking" ,rust-bitpacking-0.8) + ("rust-brotli" ,rust-brotli-3) + ("rust-flate2" ,rust-flate2-1) + ("rust-futures" ,rust-futures-0.3) + ("rust-lz4" ,rust-lz4-1) + ("rust-parquet-format-async-temp" ,rust-parquet-format-async-temp-0.2) + ("rust-snap" ,rust-snap-1) + ("rust-streaming-iterator" ,rust-streaming-iterator-0.1) + ("rust-zstd" ,rust-zstd-0.9)))) + (home-page "https://crates.io/crates/parquet2") + (synopsis "Safe implementation of Parquet IO") + (description + "Parquet2 is a re-write of the official Parquet crate with performance, +parallelism and safety in mind.") + (license license:asl2.0))) + (define-public rust-parse-zoneinfo-0.3 (package (name "rust-parse-zoneinfo") -- cgit 1.4.1 From d21a7c6cf91b5efca57d5f189392be23ca2bc43c Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 3 Nov 2021 19:40:44 +0100 Subject: gnu: Add rust-arrow2-0.5. * gnu/packages/crates-io.scm (rust-arrow2-0.5): New variable. --- gnu/packages/crates-io.scm | 49 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index f26f672f84..977d69480e 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -2496,6 +2496,55 @@ format.") ("rust-serde-derive" ,rust-serde-derive-1) ("rust-serde-json" ,rust-serde-json-1)))))) +(define-public rust-arrow2-0.5 + (package + (name "rust-arrow2") + (version "0.5.3") + (source + (origin + (method url-fetch) + (uri (crate-uri "arrow2" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "042m859jfffnhi84qc919pkyanlr98wqqf67pcrylk4hhh0v84xx")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-ahash" ,rust-ahash-0.7) + ("rust-base64" ,rust-base64-0.13) + ("rust-chrono" ,rust-chrono-0.4) + ("rust-chrono-tz" ,rust-chrono-tz-0.5) + ("rust-comfy-table" ,rust-comfy-table-4) + ("rust-csv" ,rust-csv-1) + ("rust-flatbuffers" ,rust-flatbuffers-2) + ("rust-futures" ,rust-futures-0.3) + ("rust-hash-hasher" ,rust-hash-hasher-2) + ("rust-hex" ,rust-hex-0.4) + ("rust-indexmap" ,rust-indexmap-1) + ("rust-itertools" ,rust-itertools-0.10) + ("rust-lazy-static" ,rust-lazy-static-1) + ("rust-lexical-core" ,rust-lexical-core-0.8) + ("rust-lz4" ,rust-lz4-1) + ("rust-multiversion" ,rust-multiversion-0.6) + ("rust-num-traits" ,rust-num-traits-0.2) + ("rust-packed-simd-2" ,rust-packed-simd-2-0.3) + ("rust-parquet2" ,rust-parquet2-0.4) + ("rust-rand" ,rust-rand-0.8) + ("rust-regex" ,rust-regex-1) + ("rust-serde" ,rust-serde-1) + ("rust-serde-derive" ,rust-serde-derive-1) + ("rust-serde-json" ,rust-serde-json-1) + ("rust-streaming-iterator" ,rust-streaming-iterator-0.1) + ("rust-strength-reduce" ,rust-strength-reduce-0.2) + ("rust-zstd" ,rust-zstd-0.9)))) + (home-page "https://github.com/jorgecarleitao/arrow2") + (synopsis "Unofficial implementation of Apache Arrow spec in safe Rust") + (description + "Arrow2 is a Rust library to work with the Arrow format. It is +a re-write of the official Arrow crate using transmute-free operations.") + (license license:asl2.0))) + (define-public rust-article-scraper-1 (package (name "rust-article-scraper") -- cgit 1.4.1 From bc85e5c072c3b3406906e698edf9e30a7993bb3c Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 21:48:37 +0200 Subject: gnu: Add rust-polars-arrow-0.16. * gnu/packages/crates-io.scm (rust-polars-arrow-0.16): New variable. (rust-polars-arrow-0.15): Inherit from above. --- gnu/packages/crates-io.scm | 27 +++++++++++++++++++++++---- 1 file changed, 23 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 977d69480e..da623510e5 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -35759,22 +35759,22 @@ applications.") ("rust-polars-io" ,rust-polars-io-0.13) ("rust-polars-lazy" ,rust-polars-lazy-0.13)))))) -(define-public rust-polars-arrow-0.15 +(define-public rust-polars-arrow-0.16 (package (name "rust-polars-arrow") - (version "0.15.1") + (version "0.16.0") (source (origin (method url-fetch) (uri (crate-uri "polars-arrow" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "0d8ir9dajywfqg6ck557vbvzsdmndc1ipn9mgrqi15yini1qmw2z")))) + (base32 "0pwx7nsayn526r9gw16yzqq3r6mn6ivcdxzsj8737whk04qy3ssb")))) (build-system cargo-build-system) (arguments `(#:skip-build? #t #:cargo-inputs - (("rust-arrow" ,rust-arrow-5) + (("rust-arrow2" ,rust-arrow2-0.5) ("rust-num" ,rust-num-0.4) ("rust-thiserror" ,rust-thiserror-1)))) (home-page "https://github.com/ritchie46/polars") @@ -35783,6 +35783,25 @@ applications.") "This crate provides Arrow interfaces for Polars DataFrame library.") (license license:expat))) +(define-public rust-polars-arrow-0.15 + (package + (inherit rust-polars-arrow-0.16) + (name "rust-polars-arrow") + (version "0.15.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "polars-arrow" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0d8ir9dajywfqg6ck557vbvzsdmndc1ipn9mgrqi15yini1qmw2z")))) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-arrow" ,rust-arrow-5) + ("rust-num" ,rust-num-0.4) + ("rust-thiserror" ,rust-thiserror-1)))))) + (define-public rust-polars-arrow-0.14 (package (inherit rust-polars-arrow-0.15) -- cgit 1.4.1 From 4bbb2248c429f5008458b77639fa05c2830b8157 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 21:49:17 +0200 Subject: gnu: Add rust-polars-core-0.16. * gnu/packages/crates-io.scm (rust-polars-core-0.16): New variable. (rust-polars-core-0.15): Inherit from above. --- gnu/packages/crates-io.scm | 50 ++++++++++++++++++++++++++++++++++++++++------ 1 file changed, 44 insertions(+), 6 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index da623510e5..f167677546 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -35841,24 +35841,24 @@ applications.") ("rust-num" ,rust-num-0.4) ("rust-thiserror" ,rust-thiserror-1)))))) -(define-public rust-polars-core-0.15 +(define-public rust-polars-core-0.16 (package (name "rust-polars-core") - (version "0.15.1") + (version "0.16.0") (source (origin (method url-fetch) (uri (crate-uri "polars-core" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "0vzyyqg0s6h3k77z7nkmqrrgnp7nbi7sh5nmlw1ggrlml9ps0aa9")))) + (base32 "0knhxc2b0k5jpvm7fxm64b5hjdyqgxjjyi6cnsiy5sya3mj3v9cd")))) (build-system cargo-build-system) (arguments `(#:skip-build? #t #:cargo-inputs (("rust-ahash" ,rust-ahash-0.7) ("rust-anyhow" ,rust-anyhow-1) - ("rust-arrow" ,rust-arrow-5) + ("rust-arrow2" ,rust-arrow2-0.5) ("rust-chrono" ,rust-chrono-0.4) ("rust-comfy-table" ,rust-comfy-table-1) ("rust-hashbrown" ,rust-hashbrown-0.11) @@ -35868,8 +35868,7 @@ applications.") ("rust-ndarray" ,rust-ndarray-0.15) ("rust-num" ,rust-num-0.4) ("rust-num-cpus" ,rust-num-cpus-1) - ("rust-parquet" ,rust-parquet-5) - ("rust-polars-arrow" ,rust-polars-arrow-0.15) + ("rust-polars-arrow" ,rust-polars-arrow-0.16) ("rust-prettytable-rs" ,rust-prettytable-rs-0.8) ("rust-rand" ,rust-rand-0.7) ("rust-rand-distr" ,rust-rand-distr-0.3) @@ -35885,6 +35884,45 @@ applications.") "This crate provides the core of the Polars DataFrame library.") (license license:expat))) +(define-public rust-polars-core-0.15 + (package + (inherit rust-polars-core-0.16) + (name "rust-polars-core") + (version "0.15.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "polars-core" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0vzyyqg0s6h3k77z7nkmqrrgnp7nbi7sh5nmlw1ggrlml9ps0aa9")))) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-ahash" ,rust-ahash-0.7) + ("rust-anyhow" ,rust-anyhow-1) + ("rust-arrow" ,rust-arrow-5) + ("rust-chrono" ,rust-chrono-0.4) + ("rust-comfy-table" ,rust-comfy-table-1) + ("rust-hashbrown" ,rust-hashbrown-0.11) + ("rust-itertools" ,rust-itertools-0.10) + ("rust-jsonpath-lib" ,rust-jsonpath-lib-0.3) + ("rust-lazy-static" ,rust-lazy-static-1) + ("rust-ndarray" ,rust-ndarray-0.15) + ("rust-num" ,rust-num-0.4) + ("rust-num-cpus" ,rust-num-cpus-1) + ("rust-parquet" ,rust-parquet-5) + ("rust-polars-arrow" ,rust-polars-arrow-0.15) + ("rust-prettytable-rs" ,rust-prettytable-rs-0.8) + ("rust-rand" ,rust-rand-0.7) + ("rust-rand-distr" ,rust-rand-distr-0.3) + ("rust-rayon" ,rust-rayon-1) + ("rust-regex" ,rust-regex-1) + ("rust-serde" ,rust-serde-1) + ("rust-serde-json" ,rust-serde-json-1) + ("rust-thiserror" ,rust-thiserror-1) + ("rust-unsafe-unwrap" ,rust-unsafe-unwrap-0.1)))))) + (define-public rust-polars-core-0.14 (package (inherit rust-polars-core-0.15) -- cgit 1.4.1 From 0c5a066d5cb0d5250857724635c9560915068c8b Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 21:50:33 +0200 Subject: gnu: Add rust-polars-io-0.16. * gnu/packages/crates-io.scm (rust-polars-io-0.16): New variable. (rust-polars-io-0.15): Inherit from above. --- gnu/packages/crates-io.scm | 46 +++++++++++++++++++++++++++++++++++++++------- 1 file changed, 39 insertions(+), 7 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index f167677546..1527438d09 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -35998,8 +35998,46 @@ applications.") ("rust-thiserror" ,rust-thiserror-1) ("rust-unsafe-unwrap" ,rust-unsafe-unwrap-0.1)))))) +(define-public rust-polars-io-0.16 + (package + (name "rust-polars-io") + (version "0.16.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "polars-io" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0yqpjk0ymqpjq6f0mnm9hhw9xmjradx6vqzg5n54qvl6v3s3p3kh")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-ahash" ,rust-ahash-0.7) + ("rust-anyhow" ,rust-anyhow-1) + ("rust-arrow2" ,rust-arrow2-0.5) + ("rust-csv-core" ,rust-csv-core-0.1) + ("rust-dirs" ,rust-dirs-3) + ("rust-flate2" ,rust-flate2-1) + ("rust-lazy-static" ,rust-lazy-static-1) + ("rust-lexical" ,rust-lexical-6) + ("rust-memmap2" ,rust-memmap2-0.2) + ("rust-num" ,rust-num-0.4) + ("rust-num-cpus" ,rust-num-cpus-1) + ("rust-polars-arrow" ,rust-polars-arrow-0.16) + ("rust-polars-core" ,rust-polars-core-0.16) + ("rust-rayon" ,rust-rayon-1) + ("rust-regex" ,rust-regex-1) + ("rust-simdutf8" ,rust-simdutf8-0.1)))) + (home-page "https://github.com/ritchie46/polars") + (synopsis "IO related logic for the Polars DataFrame library") + (description + "This crate provides IO related logic for the Polars DataFrame library.") + (license license:expat))) + (define-public rust-polars-io-0.15 (package + (inherit rust-polars-io-0.16) (name "rust-polars-io") (version "0.15.1") (source @@ -36009,7 +36047,6 @@ applications.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 "19r2l3rxjdk25ir93l85ap4q0w5p7apjw3g57pszxph9nh2j8ba2")))) - (build-system cargo-build-system) (arguments `(#:skip-build? #t #:cargo-inputs @@ -36030,12 +36067,7 @@ applications.") ("rust-polars-core" ,rust-polars-core-0.15) ("rust-rayon" ,rust-rayon-1) ("rust-regex" ,rust-regex-1) - ("rust-simdutf8" ,rust-simdutf8-0.1)))) - (home-page "https://github.com/ritchie46/polars") - (synopsis "IO related logic for the Polars DataFrame library") - (description - "This crate provides IO related logic for the Polars DataFrame library.") - (license license:expat))) + ("rust-simdutf8" ,rust-simdutf8-0.1)))))) (define-public rust-polars-io-0.14 (package -- cgit 1.4.1 From d2c7e9c0575b5d985d547e91c9fb0f6d7747ca9c Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 21:51:21 +0200 Subject: gnu: Add rust-polars-lazy-0.16. * gnu/packages/crates-io.scm (rust-polars-lazy-0.16): New variable. (rust-polars-lazy-0.15): Inherit from above. --- gnu/packages/crates-io.scm | 35 +++++++++++++++++++++++++++++------ 1 file changed, 29 insertions(+), 6 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 1527438d09..68e29ac9c0 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -36136,26 +36136,26 @@ applications.") ("rust-rayon" ,rust-rayon-1) ("rust-regex" ,rust-regex-1)))))) -(define-public rust-polars-lazy-0.15 +(define-public rust-polars-lazy-0.16 (package (name "rust-polars-lazy") - (version "0.15.1") + (version "0.16.0") (source (origin (method url-fetch) (uri (crate-uri "polars-lazy" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "0xh3a0gjsisx62zwjmawxg9giin7bwmh7z7y4cc2d3ygy8nk19jh")))) + (base32 "01bjsk880dvigyqx7aj3f8zvxpk9gl14k3s40w3dv3aanhdzq7wx")))) (build-system cargo-build-system) (arguments `(#:skip-build? #t #:cargo-inputs (("rust-ahash" ,rust-ahash-0.7) ("rust-itertools" ,rust-itertools-0.10) - ("rust-polars-arrow" ,rust-polars-arrow-0.15) - ("rust-polars-core" ,rust-polars-core-0.15) - ("rust-polars-io" ,rust-polars-io-0.15) + ("rust-polars-arrow" ,rust-polars-arrow-0.16) + ("rust-polars-core" ,rust-polars-core-0.16) + ("rust-polars-io" ,rust-polars-io-0.16) ("rust-rayon" ,rust-rayon-1) ("rust-regex" ,rust-regex-1)))) (home-page "https://github.com/ritchie46/polars") @@ -36165,6 +36165,29 @@ applications.") library.") (license license:expat))) +(define-public rust-polars-lazy-0.15 + (package + (inherit rust-polars-lazy-0.16) + (name "rust-polars-lazy") + (version "0.15.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "polars-lazy" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0xh3a0gjsisx62zwjmawxg9giin7bwmh7z7y4cc2d3ygy8nk19jh")))) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-ahash" ,rust-ahash-0.7) + ("rust-itertools" ,rust-itertools-0.10) + ("rust-polars-arrow" ,rust-polars-arrow-0.15) + ("rust-polars-core" ,rust-polars-core-0.15) + ("rust-polars-io" ,rust-polars-io-0.15) + ("rust-rayon" ,rust-rayon-1) + ("rust-regex" ,rust-regex-1)))))) + (define-public rust-polars-lazy-0.14 (package (inherit rust-polars-lazy-0.15) -- cgit 1.4.1 From 5da0efbe9e84565a9bbd70e0a1ac691a2f6636cc Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 6 Oct 2021 21:52:10 +0200 Subject: gnu: Add rust-polars-0.16. * gnu/packages/crates-io.scm (rust-polars-0.16): New variable. (rust-polars-0.15): Inherit from above. --- gnu/packages/crates-io.scm | 31 +++++++++++++++++++++++++------ 1 file changed, 25 insertions(+), 6 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 68e29ac9c0..e57abb404c 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -35695,30 +35695,49 @@ applications.") "Additional trait for Read and Write to read and write Plain Old Data.") (license (list license:expat license:asl2.0)))) -(define-public rust-polars-0.15 +(define-public rust-polars-0.16 (package (name "rust-polars") - (version "0.15.1") + (version "0.16.0") (source (origin (method url-fetch) (uri (crate-uri "polars" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "1sl7vs6ck05f8w8jp7v75431b4v5j2rvvvw53jqgxc5226i7a2h8")))) + (base32 "1s4fqc3vlpz73dbagfsj3hx7y7xmpqnp7nj0cn9srijxgxq5nm73")))) (build-system cargo-build-system) (arguments `(#:skip-build? #t #:cargo-inputs - (("rust-polars-core" ,rust-polars-core-0.15) - ("rust-polars-io" ,rust-polars-io-0.15) - ("rust-polars-lazy" ,rust-polars-lazy-0.15)))) + (("rust-polars-core" ,rust-polars-core-0.16) + ("rust-polars-io" ,rust-polars-io-0.16) + ("rust-polars-lazy" ,rust-polars-lazy-0.16)))) (home-page "https://github.com/ritchie46/polars") (synopsis "DataFrame Library based on Apache Arrow") (description "Polars is a dataframe Library based on Apache Arrow.") (license license:expat))) +(define-public rust-polars-0.15 + (package + (inherit rust-polars-0.16) + (name "rust-polars") + (version "0.15.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "polars" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1sl7vs6ck05f8w8jp7v75431b4v5j2rvvvw53jqgxc5226i7a2h8")))) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-polars-core" ,rust-polars-core-0.15) + ("rust-polars-io" ,rust-polars-io-0.15) + ("rust-polars-lazy" ,rust-polars-lazy-0.15)))))) + (define-public rust-polars-0.14 (package (inherit rust-polars-0.15) -- cgit 1.4.1 From a18fea500986efa1209fd18a021a7873828f7312 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 3 Nov 2021 23:09:36 +0100 Subject: Revert "gnu: Add rust-sysinfo-0.20." This reverts commit cc415fd880fea9059e6d0bd4c45ce143126d9f14. Rust 1.54 is not yet packages. --- gnu/packages/crates-io.scm | 35 +++++------------------------------ 1 file changed, 5 insertions(+), 30 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index e57abb404c..b229683ab4 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -50308,10 +50308,10 @@ no_std compatible by default, only relying on alloc.") ("rust-errno" ,rust-errno-0.2) ("rust-libc" ,rust-libc-0.2)))))) -(define-public rust-sysinfo-0.20 +(define-public rust-sysinfo-0.18 (package (name "rust-sysinfo") - (version "0.20.3") + (version "0.18.2") (source (origin (method url-fetch) @@ -50319,14 +50319,15 @@ no_std compatible by default, only relying on alloc.") (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "0ljf8cdn50g9vrg4h9qxv070n4zd83cv63g62007qs8d8n1pimwj")))) + (base32 + "0zd974yydc4yszxgx9hiqm5ah2rqnsgyq3qrl7raf90scpxaw16l")))) (build-system cargo-build-system) (arguments `(#:skip-build? #t - #:rust ,rust-1.54 #:cargo-inputs (("rust-cfg-if" ,rust-cfg-if-1) ("rust-core-foundation-sys" ,rust-core-foundation-sys-0.8) + ("rust-doc-comment" ,rust-doc-comment-0.3) ("rust-libc" ,rust-libc-0.2) ("rust-ntapi" ,rust-ntapi-0.3) ("rust-once-cell" ,rust-once-cell-1) @@ -50339,32 +50340,6 @@ no_std compatible by default, only relying on alloc.") processors, disks, components and networks.") (license license:expat))) -(define-public rust-sysinfo-0.18 - (package - (inherit rust-sysinfo-0.20) - (name "rust-sysinfo") - (version "0.18.2") - (source - (origin - (method url-fetch) - (uri (crate-uri "sysinfo" version)) - (file-name - (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "0zd974yydc4yszxgx9hiqm5ah2rqnsgyq3qrl7raf90scpxaw16l")))) - (arguments - `(#:skip-build? #t - #:cargo-inputs - (("rust-cfg-if" ,rust-cfg-if-1) - ("rust-core-foundation-sys" ,rust-core-foundation-sys-0.8) - ("rust-doc-comment" ,rust-doc-comment-0.3) - ("rust-libc" ,rust-libc-0.2) - ("rust-ntapi" ,rust-ntapi-0.3) - ("rust-once-cell" ,rust-once-cell-1) - ("rust-rayon" ,rust-rayon-1) - ("rust-winapi" ,rust-winapi-0.3)))))) - (define-public rust-sysinfo-0.16 (package (inherit rust-sysinfo-0.18) -- cgit 1.4.1 From 347227efc13d3389f1a40084ea28297ce1a9e14d Mon Sep 17 00:00:00 2001 From: phodina Date: Wed, 3 Nov 2021 14:17:39 +0000 Subject: gnu: flightgear: Update to 2020.3.11. * gnu/packages/games.scm (simgear, flightgear): Update to 2020.3.11. (flightgear-data): Update uri. Signed-off-by: Efraim Flashner --- gnu/packages/games.scm | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index a1f6deb044..48722230c4 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -9261,7 +9261,7 @@ levels to unlock.") (define simgear (package (name "simgear") - (version "2018.3.5") + (version "2020.3.11") (source (origin (method url-fetch) @@ -9269,7 +9269,7 @@ levels to unlock.") (version-major+minor version) "/" "simgear-" version ".tar.bz2")) (sha256 - (base32 "1vkqm66r1205k3hdjmx5wmx5kvmsb0dgfzrs8n5gqnxj8szs42dl")))) + (base32 "0g2g3n3sb6kdimvcrn9kvlhyyrp5c6lx20fgzz8l609v5aygr3dv")))) (build-system cmake-build-system) (arguments `(#:phases @@ -9305,7 +9305,7 @@ and also provides the base for the FlightGear Flight Simulator.") (version-major+minor version) "/" "flightgear-" version ".tar.bz2")) (sha256 - (base32 "0ya3vb539kwi1qrifqhsj5j3k4w6s06hrllp2vdzxf6id7cgf0hc")) + (base32 "15sar94x13j2y1m6adgmz2q1m1i9bzj3sxqla6y3m9vyf33hc9zy")) (modules '((guix build utils))) (snippet '(begin @@ -9375,10 +9375,10 @@ and also provides the base for the FlightGear Flight Simulator.") (method url-fetch) (uri (string-append "mirror://sourceforge/flightgear/release-" (version-major+minor version) "/" - "FlightGear-" version "-data.tar.bz2")) + "FlightGear-" version "-data.txz")) (sha256 (base32 - "04fv9za5zlyxlyfh6jx78y42l3jazvzl9dq2y6rzxqlcc9g5swhk")))))) + "0n5mw9vw1snab16c1y3i9ylkiv54az57bs2mvpq20hhg5hdiagqj")))))) (home-page "https://home.flightgear.org/") (synopsis "Flight simulator") (description "The goal of the FlightGear project is to create a -- cgit 1.4.1 From 3a5b1cc32a4f9dd1128f373c087d37aad95ed309 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 3 Nov 2021 22:00:01 +0200 Subject: gnu: flightgear: Build with qt-build-system. * gnu/packages/games.scm (flightgear)[build-system]: Switch to qt-build-system. [arguments]: Remove 'wrap-executable phase. --- gnu/packages/games.scm | 19 ++----------------- 1 file changed, 2 insertions(+), 17 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 48722230c4..f601e96035 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -9313,7 +9313,7 @@ and also provides the base for the FlightGear Flight Simulator.") (for-each delete-file-recursively '("3rdparty/sqlite3/")) #t)))) - (build-system cmake-build-system) + (build-system qt-build-system) (arguments `(#:configure-flags (list "-DSYSTEM_SQLITE=ON" @@ -9325,21 +9325,6 @@ and also provides the base for the FlightGear Flight Simulator.") #:tests? #f #:phases (modify-phases %standard-phases - (add-after 'install 'wrap-executable - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (wrap-program (string-append out "/bin/fgfs") - `("QT_PLUGIN_PATH" ":" prefix - ,(map (lambda (label) - (string-append (assoc-ref inputs label) - "/lib/qt5/plugins")) - '("qtbase" "qtdeclarative" "qtsvg"))) - `("QML2_IMPORT_PATH" ":" prefix - ,(map (lambda (label) - (string-append (assoc-ref inputs label) - "/lib/qt5/qml")) - '("qtdeclarative" "qtsvg")))) - #t))) (add-after 'install 'install-data (lambda* (#:key inputs outputs #:allow-other-keys) (let ((share (string-append (assoc-ref outputs "out") "/share/flightgear"))) @@ -9379,7 +9364,7 @@ and also provides the base for the FlightGear Flight Simulator.") (sha256 (base32 "0n5mw9vw1snab16c1y3i9ylkiv54az57bs2mvpq20hhg5hdiagqj")))))) - (home-page "https://home.flightgear.org/") + (home-page "https://www.flightgear.org/") (synopsis "Flight simulator") (description "The goal of the FlightGear project is to create a sophisticated flight simulator framework for use in research or academic -- cgit 1.4.1 From 230b34cb5c88bcfda155094fde85a0a125f490f2 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 3 Nov 2021 22:01:23 +0200 Subject: gnu: simgear: Honor #:tests? flag. * gnu/packages/games.scm (simgear)[arguments]: Adjust custom 'check phase to honor the #:tests? flag. --- gnu/packages/games.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index f601e96035..b1de90cf24 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -9275,9 +9275,10 @@ levels to unlock.") `(#:phases (modify-phases %standard-phases (replace 'check - (lambda _ - ;; Skip tests that require internet access. - (invoke "ctest" "-E" "(http|dns)")))))) + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; Skip tests that require internet access. + (invoke "ctest" "-E" "(http|dns)"))))))) (inputs `(("boost" ,boost-for-mysql) ; fails with 1.69 ("curl" ,curl) -- cgit 1.4.1 From aae82f2a9587bf5c9f0af21be26e38e3bd941a84 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 3 Nov 2021 22:10:34 +0200 Subject: gnu: flightgear: Build with newer inputs. * gnu/packages/games.scm (flightgear)[inputs]: Replace openscenegraph-3.4 with openscenegraph, boost-for-mysql with boost. (simgear)[inputs]: Same. --- gnu/packages/games.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index b1de90cf24..1ea1846c0a 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -9280,12 +9280,12 @@ levels to unlock.") ;; Skip tests that require internet access. (invoke "ctest" "-E" "(http|dns)"))))))) (inputs - `(("boost" ,boost-for-mysql) ; fails with 1.69 + `(("boost" ,boost) ("curl" ,curl) ("expat" ,expat) ("mesa" ,mesa) ("openal" ,openal) - ("openscenegraph" ,openscenegraph-3.4) + ("openscenegraph" ,openscenegraph) ("zlib" ,zlib))) (home-page "https://home.flightgear.org/") (synopsis "Libraries for 3D simulations and games") @@ -9335,7 +9335,7 @@ and also provides the base for the FlightGear Flight Simulator.") "--strip-components=1"))) #t))))) (inputs - `(("boost" ,boost-for-mysql) ; same as simgear + `(("boost" ,boost) ("dbus" ,dbus) ("eudev" ,eudev) ("freeglut" ,freeglut) @@ -9343,7 +9343,7 @@ and also provides the base for the FlightGear Flight Simulator.") ("glew" ,glew) ("libpng" ,libpng) ("openal" ,openal) - ("openscenegraph" ,openscenegraph-3.4) + ("openscenegraph" ,openscenegraph) ("plib" ,plib) ("qtbase" ,qtbase-5) ("qtdeclarative" ,qtdeclarative) -- cgit 1.4.1 From ea173bd87414f72ce61c0436b9503bef7f1beb45 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 3 Nov 2021 22:11:57 +0200 Subject: gnu: Remove openscenegraph-3.4. * gnu/packages/graphics.scm (openscenegraph-3.4): Remove variable. --- gnu/packages/graphics.scm | 26 -------------------------- 1 file changed, 26 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm index 402a7406a7..aa026c60e3 100644 --- a/gnu/packages/graphics.scm +++ b/gnu/packages/graphics.scm @@ -1284,32 +1284,6 @@ virtual reality, scientific visualization and modeling.") ;; LGPL 2.1, but with 4 exceptions. This version is called OSGPL. (license license:lgpl2.1))) -;; We need this for simgear -(define-public openscenegraph-3.4 - (package (inherit openscenegraph) - (name "openscenegraph") - (version "3.4.1") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/openscenegraph/OpenSceneGraph") - (commit (string-append "OpenSceneGraph-" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1fbzg1ihjpxk6smlq80p3h3ggllbr16ihd2fxpfwzam8yr8yxip9")))) - (arguments - (substitute-keyword-arguments (package-arguments openscenegraph) - ((#:configure-flags flags) - `(cons - ;; The jpeg plugin requires conversion between integers and booleans - "-DCMAKE_CXX_FLAGS=-fpermissive" - ,flags)))) - (inputs - `(("libjpeg" ,libjpeg-turbo) - ,@(package-inputs openscenegraph))))) - (define-public gr-framework (package (name "gr-framework") -- cgit 1.4.1 From d3abd5cd8b16a9a4121da08a2778dd8a3b9cbae6 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 3 Nov 2021 22:27:21 +0200 Subject: gnu: simgear: Remove bundled expat. * gnu/packages/games.scm (simgear)[source]: Add snippet to remove bundled expat. [arguments]: Add configure-flag to use system expat. --- gnu/packages/games.scm | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 1ea1846c0a..df32a6b27d 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -9269,10 +9269,18 @@ levels to unlock.") (version-major+minor version) "/" "simgear-" version ".tar.bz2")) (sha256 - (base32 "0g2g3n3sb6kdimvcrn9kvlhyyrp5c6lx20fgzz8l609v5aygr3dv")))) + (base32 "0g2g3n3sb6kdimvcrn9kvlhyyrp5c6lx20fgzz8l609v5aygr3dv")) + (modules '((guix build utils))) + (snippet + '(begin + ;; There are some bundled libraries. + (for-each delete-file-recursively + '("3rdparty/expat/")) + #t)))) (build-system cmake-build-system) (arguments - `(#:phases + `(#:configure-flags (list "-DSYSTEM_EXPAT=ON") + #:phases (modify-phases %standard-phases (replace 'check (lambda* (#:key tests? #:allow-other-keys) -- cgit 1.4.1 From b93e06a96418b7caba109cae327c3d226a33d782 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 3 Nov 2021 22:39:47 +0200 Subject: gnu: flightgear: Use system cppunit. * gnu/packages/games.scm (flightgear)[source]: Adjust snippet to remove bundled cppunit. [arguments]: Add configure-flag to use system cppunit. --- gnu/packages/games.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index df32a6b27d..7bab31f9be 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -9320,12 +9320,14 @@ and also provides the base for the FlightGear Flight Simulator.") '(begin ;; There are some bundled libraries. (for-each delete-file-recursively - '("3rdparty/sqlite3/")) + '("3rdparty/sqlite3/" + "3rdparty/cppunit/")) #t)))) (build-system qt-build-system) (arguments `(#:configure-flags (list "-DSYSTEM_SQLITE=ON" + "-DSYSTEM_CPPUNIT=ON" (string-append "-DFG_DATA_DIR=" (assoc-ref %outputs "out") "/share/flightgear")) -- cgit 1.4.1 From 19c38b2acc99644c4104c8526d2586b3ee67f5a7 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 3 Nov 2021 23:56:01 +0200 Subject: gnu: flightgear: Prepare to run test suite. * gnu/packages/games.scm (flightgear)[arguments]: Add phase to build test binary. Add phase to skip some failing tests. Move 'check phase to after 'install-data. --- gnu/packages/games.scm | 18 ++++++++++++++++-- 1 file changed, 16 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 7bab31f9be..eb3db37c46 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -9331,11 +9331,25 @@ and also provides the base for the FlightGear Flight Simulator.") (string-append "-DFG_DATA_DIR=" (assoc-ref %outputs "out") "/share/flightgear")) - ;; TODO: test cannot be run because the "run_test_suite" executable - ;; does not seem to be built. + ;; TODO: test suite segfaults. #:tests? #f #:phases (modify-phases %standard-phases + (add-after 'unpack 'skip-some-tests + (lambda _ + (substitute* "test_suite/unit_tests/Instrumentation/test_gps.hxx" + (("CPPUNIT_TEST\\(testLongLegWestbound\\);" all) + (string-append "// " all)) + (("CPPUNIT_TEST\\(testFinalLegCourse\\);" all) + (string-append "// " all))))) + (add-after 'build 'build-test-suite + (lambda* args + ((assoc-ref %standard-phases 'build) + #:make-flags (list "fgfs_test_suite")))) + ;; Test suite needs access to FGData so run it after 'install. + (delete 'check) + (add-after 'install-data 'check + (assoc-ref %standard-phases 'check)) (add-after 'install 'install-data (lambda* (#:key inputs outputs #:allow-other-keys) (let ((share (string-append (assoc-ref outputs "out") "/share/flightgear"))) -- cgit 1.4.1 From 8d2e77bf45027e393c9716c0460fc20871be904a Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 3 Nov 2021 02:23:49 -0400 Subject: gnu: linux-libre: Update to 5.14.16. * gnu/packages/linux.scm (linux-libre-5.14-version): Update to 5.14.16. (linux-libre-5.14-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 4a3b7b6cf4..414f9d3844 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -347,7 +347,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The current "stable" kernels. That is, the most recently released major ;; versions that are still supported upstream. -(define-public linux-libre-5.14-version "5.14.15") +(define-public linux-libre-5.14-version "5.14.16") (define-public linux-libre-5.14-gnu-revision "gnu") (define deblob-scripts-5.14 (linux-libre-deblob-scripts @@ -357,7 +357,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "024rz0bp3n3r5nkwbib7byx10d72c2fh5cw9iv00diyzgnp819g7"))) (define-public linux-libre-5.14-pristine-source (let ((version linux-libre-5.14-version) - (hash (base32 "01m4qw1z7xn3ngsbm1bvcvikqpkjjr9n8585556wkmz9d469mwvl"))) + (hash (base32 "005wis2y5dhksb6n0r4p3xjldppmdnd360dhxa04rfc4z2qwn3f3"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.14))) -- cgit 1.4.1 From e3ccd6ade8ae82e9774f2fc8563badb1e65a5271 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 3 Nov 2021 02:33:32 -0400 Subject: gnu: linux-libre 5.10: Update to 5.10.77. * gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.77. (linux-libre-5.10-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 414f9d3844..961f15d543 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -365,7 +365,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The "longterm" kernels — the older releases with long-term upstream support. ;; Here are the support timelines: ;; -(define-public linux-libre-5.10-version "5.10.76") +(define-public linux-libre-5.10-version "5.10.77") (define-public linux-libre-5.10-gnu-revision "gnu1") (define deblob-scripts-5.10 (linux-libre-deblob-scripts @@ -375,7 +375,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "024rz0bp3n3r5nkwbib7byx10d72c2fh5cw9iv00diyzgnp819g7"))) (define-public linux-libre-5.10-pristine-source (let ((version linux-libre-5.10-version) - (hash (base32 "140qkvs88b5zh6mxxzpf36z1r8bbvyh3yigripqjz1k236x0j2j8"))) + (hash (base32 "1hwgbcfv9wfx9ka25lsqjrnzskynfgmswcyp5vk14wnxq7glxdnk"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.10))) -- cgit 1.4.1 From fd7b06f40e4b9c3c811364e7c30260df475c6f71 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 3 Nov 2021 02:33:48 -0400 Subject: gnu: linux-libre 5.4: Update to 5.4.157. * gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.157. (linux-libre-5.4-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 961f15d543..9323223adc 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -380,7 +380,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-5.10))) -(define-public linux-libre-5.4-version "5.4.156") +(define-public linux-libre-5.4-version "5.4.157") (define-public linux-libre-5.4-gnu-revision "gnu1") (define deblob-scripts-5.4 (linux-libre-deblob-scripts @@ -390,7 +390,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1a0k9i8gnzkyvfr80f8xw2fnxfwddhz1pzicz9fh0y3jzzkzk45p"))) (define-public linux-libre-5.4-pristine-source (let ((version linux-libre-5.4-version) - (hash (base32 "1zkpqfhrc5n0yiij3jzvzywgabva53c8668f1ly1pkrzcbj77zh6"))) + (hash (base32 "0jl62j22vs59bc90mvzavv0ii9hvk436pbnrpqf3x9f8nfybngwz"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.4))) -- cgit 1.4.1 From 37757fd6b99e62c3ead8920fd26a2ec52c02a4ad Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 3 Nov 2021 02:34:05 -0400 Subject: gnu: linux-libre 4.19: Update to 4.19.215. * gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.215. (linux-libre-4.19-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 9323223adc..b814b86d5b 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -395,7 +395,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-5.4))) -(define-public linux-libre-4.19-version "4.19.214") +(define-public linux-libre-4.19-version "4.19.215") (define-public linux-libre-4.19-gnu-revision "gnu1") (define deblob-scripts-4.19 (linux-libre-deblob-scripts @@ -405,7 +405,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1a0k9i8gnzkyvfr80f8xw2fnxfwddhz1pzicz9fh0y3jzzkzk45p"))) (define-public linux-libre-4.19-pristine-source (let ((version linux-libre-4.19-version) - (hash (base32 "0i08np4gxiks7chp6j328pdqb02apbba53mj4zvxb9v37qpxzqgz"))) + (hash (base32 "1czjqa5wbsmzgl7wwqlp9qbdig45ibq11m9pcykrjaclrgwn884y"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.19))) -- cgit 1.4.1 From deb34d242b6d1d14c8fae889619479ec0592dfd9 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 3 Nov 2021 02:34:23 -0400 Subject: gnu: linux-libre 4.14: Update to 4.14.254. * gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.254. (linux-libre-4.14-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index b814b86d5b..814e60a12d 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -410,7 +410,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-4.19))) -(define-public linux-libre-4.14-version "4.14.253") +(define-public linux-libre-4.14-version "4.14.254") (define-public linux-libre-4.14-gnu-revision "gnu1") (define deblob-scripts-4.14 (linux-libre-deblob-scripts @@ -420,7 +420,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1a0k9i8gnzkyvfr80f8xw2fnxfwddhz1pzicz9fh0y3jzzkzk45p"))) (define-public linux-libre-4.14-pristine-source (let ((version linux-libre-4.14-version) - (hash (base32 "1mgl55c8fa2ry4qp0phkdkzjhwfnkbhvi266n348kyjyqnjl234f"))) + (hash (base32 "0ihdlsg4jg9wwhhcbjjmrcchnl9pc0szh21nwmbhwnxgqcdmrnfz"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.14))) -- cgit 1.4.1 From 20b93133e2c6b706507989ac5491b0434aa828c9 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 3 Nov 2021 02:34:38 -0400 Subject: gnu: linux-libre 4.9: Update to 4.9.289. * gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.289. (linux-libre-4.9-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 814e60a12d..ad0de4728f 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -425,7 +425,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-4.14))) -(define-public linux-libre-4.9-version "4.9.288") +(define-public linux-libre-4.9-version "4.9.289") (define-public linux-libre-4.9-gnu-revision "gnu1") (define deblob-scripts-4.9 (linux-libre-deblob-scripts @@ -435,7 +435,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1a0k9i8gnzkyvfr80f8xw2fnxfwddhz1pzicz9fh0y3jzzkzk45p"))) (define-public linux-libre-4.9-pristine-source (let ((version linux-libre-4.9-version) - (hash (base32 "0v5592v565bl924c23m1n7p5zddr0w7zn8m97pmikk6p7cyhjq9n"))) + (hash (base32 "19kz74qgw5yzfinnsvljmn2zm855lr4cxgfpn8gwljmkspyx1hm5"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.9))) -- cgit 1.4.1 From 63c356fe13f0c7cc560a1f9aeec4926422c22137 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 3 Nov 2021 02:34:54 -0400 Subject: gnu: linux-libre 4.4: Update to 4.4.291. * gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.291. (linux-libre-4.4-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index ad0de4728f..949d415db1 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -440,7 +440,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-4.9))) -(define-public linux-libre-4.4-version "4.4.290") +(define-public linux-libre-4.4-version "4.4.291") (define-public linux-libre-4.4-gnu-revision "gnu1") (define deblob-scripts-4.4 (linux-libre-deblob-scripts @@ -450,7 +450,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1a0k9i8gnzkyvfr80f8xw2fnxfwddhz1pzicz9fh0y3jzzkzk45p"))) (define-public linux-libre-4.4-pristine-source (let ((version linux-libre-4.4-version) - (hash (base32 "1dcx58nmzkcc5nz2b5b7mgw4w7y28v3s9wd8h78czdqfa0kxrl20"))) + (hash (base32 "0lbbvv3ha4d8nwzjh8bdk0aqyd12w6gw0nsxsdnp8pbmnndgb9vh"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.4))) -- cgit 1.4.1 From 63f78f6a6ea0d33f3b1fa68c7285cfb865677211 Mon Sep 17 00:00:00 2001 From: Liliana Marie Prikler Date: Thu, 4 Nov 2021 06:08:19 +0100 Subject: gnu: webkitgtk: Use GCC 11 instead of Clang. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit WebkitGTK still compiles fine on x86_64 using GCC 11. This is the only architecture known to compile currently, as i686 fails with Clang and others fail due to unsatisfied dependencies. * gnu/packages/webkit.scm (webkitgtk)[#:phases]: Drop ‘prepare-build-environment’. [native-inputs]: Drop clang, add gcc. --- gnu/packages/webkit.scm | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/webkit.scm b/gnu/packages/webkit.scm index e54b680855..7384ead14b 100644 --- a/gnu/packages/webkit.scm +++ b/gnu/packages/webkit.scm @@ -295,11 +295,6 @@ acceleration in mind, leveraging common 3D graphics APIs for best performance.") (("libWPEBackend-fdo-([\\.0-9]+)\\.so" all version) (string-append wpebackend-fdo "/lib/" all))) #t))) - (add-before 'configure 'prepare-build-environment - (lambda* (#:key inputs #:allow-other-keys) - (setenv "CC" "clang") - (setenv "CXX" "clang++") - #t)) (add-after 'install 'move-doc-files (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out")) @@ -309,8 +304,8 @@ acceleration in mind, leveraging common 3D graphics APIs for best performance.") (string-append doc "/share/gtk-doc")) #t)))))) (native-inputs - `(("clang" ,clang-11) - ("bison" ,bison) + `(("bison" ,bison) + ("gcc" ,gcc-11) ("gettext" ,gettext-minimal) ("glib:bin" ,glib "bin") ; for glib-mkenums, etc. ("gobject-introspection" ,gobject-introspection) -- cgit 1.4.1 From fcb8888f4d129b99cf0412c942c2f4e46965b08d Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 4 Nov 2021 10:50:27 +0100 Subject: gnu: emacs-ebib: Update to 2.33. * gnu/packages/emacs-xyz.scm (emacs-ebib): Update to 2.33. --- gnu/packages/emacs-xyz.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 624fe957e3..d385da04ce 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -17684,7 +17684,7 @@ files to be expanded upon opening them.") (define-public emacs-ebib (package (name "emacs-ebib") - (version "2.32.2") + (version "2.33") (source (origin (method git-fetch) @@ -17693,10 +17693,11 @@ files to be expanded upon opening them.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "04kw0akp35r2ibrcav4kaf34d1xs8pckjiygv7h1nqpv6dmrgfq7")))) + (base32 "18gvmymkpzws8s4zjcm1kijyr55dgfcq201z3w1jzhkhcs01bfsc")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-biblio" ,emacs-biblio) + ("emacs-ivy" ,emacs-ivy) ("emacs-parsebib" ,emacs-parsebib))) (home-page "https://joostkremers.github.io/ebib/") (synopsis "BibTeX database manager for Emacs") -- cgit 1.4.1 From 72bf3c0b79f6f0e93d26c4fbd95c7039311a120e Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 4 Nov 2021 10:54:37 +0100 Subject: gnu: emacs-eshell-did-you-mean: Update to 0.2. * gnu/packages/emacs-xyz.scm (emacs-eshell-did-you-mean): Update to 0.2. --- gnu/packages/emacs-xyz.scm | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index d385da04ce..7ff478468d 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -26626,19 +26626,18 @@ available.") (define-public emacs-eshell-did-you-mean (package (name "emacs-eshell-did-you-mean") - (version "0.1") - (home-page "https://github.com/xuchunyang/eshell-did-you-mean") + (version "0.2") (source (origin (method git-fetch) (uri (git-reference - (url home-page) + (url "https://github.com/xuchunyang/eshell-did-you-mean") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 - "0v0wshck5n4hspcv1zk1g2nm6xiigcjp16lx0dc8wzkl6ymljvbg")))) + (base32 "158g8b4crm0gf5pilfxf89hdsb22gr1wbrjyx9gf45bmcll3i9vf")))) (build-system emacs-build-system) + (home-page "https://github.com/xuchunyang/eshell-did-you-mean") (synopsis "Display suggestions on 'command not found' in Eshell") (description "This library adds a list of 'Did you mean...' suggestions when the command was not found in Eshell. The suggestions are found after the -- cgit 1.4.1 From 1007eb4874b7d3d2e0ecda07157f5794a0591ea2 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Thu, 4 Nov 2021 08:27:15 -0400 Subject: Revert "gnu: webkitgtk: Use GCC 11 instead of Clang." This reverts commit 63f78f6a6ea0d33f3b1fa68c7285cfb865677211. It led to broken builds of epiphany, gnome-online-accounts, yelp, zenity, surf, and possibly others. --- gnu/packages/webkit.scm | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/webkit.scm b/gnu/packages/webkit.scm index 7384ead14b..e54b680855 100644 --- a/gnu/packages/webkit.scm +++ b/gnu/packages/webkit.scm @@ -295,6 +295,11 @@ acceleration in mind, leveraging common 3D graphics APIs for best performance.") (("libWPEBackend-fdo-([\\.0-9]+)\\.so" all version) (string-append wpebackend-fdo "/lib/" all))) #t))) + (add-before 'configure 'prepare-build-environment + (lambda* (#:key inputs #:allow-other-keys) + (setenv "CC" "clang") + (setenv "CXX" "clang++") + #t)) (add-after 'install 'move-doc-files (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out")) @@ -304,8 +309,8 @@ acceleration in mind, leveraging common 3D graphics APIs for best performance.") (string-append doc "/share/gtk-doc")) #t)))))) (native-inputs - `(("bison" ,bison) - ("gcc" ,gcc-11) + `(("clang" ,clang-11) + ("bison" ,bison) ("gettext" ,gettext-minimal) ("glib:bin" ,glib "bin") ; for glib-mkenums, etc. ("gobject-introspection" ,gobject-introspection) -- cgit 1.4.1 From 88d5081986bb1f78b37a11e9e24f5658f2315558 Mon Sep 17 00:00:00 2001 From: Morgan Smith Date: Tue, 2 Nov 2021 19:13:10 -0400 Subject: gnu: emacs-flymake-shellcheck: Add reference to shellcheck. * gnu/packages/emacs-xyz.scm (emacs-flymake-shellcheck) [inputs]: Add shellcheck. [arguments]: Add substitute-shellcheck-path phase. Signed-off-by: Efraim Flashner --- gnu/packages/emacs-xyz.scm | 13 +++++++++++++ 1 file changed, 13 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 7ff478468d..9ba178513c 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -1649,6 +1649,19 @@ boilerplate code from defining new Flymake backend functions.") (sha256 (base32 "04yfb4sy41spjzk9mhm4gy0h8vnjx09p2g6nm1yzgd9a5ph9sqgl")))) (build-system emacs-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'substitute-shellcheck-path + (lambda* (#:key inputs #:allow-other-keys) + (make-file-writable "flymake-shellcheck.el") + (emacs-substitute-sexps "flymake-shellcheck.el" + ("defcustom flymake-shellcheck-path" + `(or (executable-find "shellcheck") + ,(string-append (assoc-ref inputs "shellcheck") + "/bin/shellcheck"))))))))) + (inputs + `(("shellcheck" ,shellcheck))) (home-page "https://github.com/federicotdn/flymake-shellcheck") (synopsis "Flymake backend for Bash/Sh powered by ShellCheck") (description -- cgit 1.4.1 From 46b4f9b9a7e7fdd15bdc4562acaa816d3bf9d237 Mon Sep 17 00:00:00 2001 From: Foo Chuan Wei Date: Mon, 1 Nov 2021 04:53:38 +0000 Subject: gnu: Add vim-nerdcommenter. * gnu/packages/vim.scm (vim-nerdcommenter): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/vim.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm index f70729952d..1abfffbce2 100644 --- a/gnu/packages/vim.scm +++ b/gnu/packages/vim.scm @@ -1296,3 +1296,32 @@ a sidebar that displays the ctags-generated tags of the current file, ordered by their scope. This means that for example methods in C++ are displayed under the class they are defined in.") (license license:vim))) + +(define-public vim-nerdcommenter + (let ((commit "a65465d321f2f8a74b2ffa540b9b87563f7e12e8") + (revision "1")) + (package + (name "vim-nerdcommenter") + (version (git-version "2.5.2" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/preservim/nerdcommenter") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "00ir65iv8jfbgzjmj7332fmydh0qhabbhx8zbvd3j6pgfxqpaafw")))) + (build-system copy-build-system) + (arguments + '(#:install-plan + '(("autoload" "share/vim/vimfiles/") + ("doc" "share/vim/vimfiles/") + ("plugin" "share/vim/vimfiles/")))) + (home-page "https://github.com/preservim/nerdcommenter") + (synopsis "Vim plugin for easy commenting of code") + (description + "NERD commenter is a Vim plugin that provides many different commenting +operations and styles which are invoked via key mappings and a menu. These +operations are available for most filetypes.") + (license license:cc0)))) -- cgit 1.4.1 From d45e823047586bbed1c58f6b721f131b3653367b Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 4 Nov 2021 15:28:22 +0100 Subject: gnu: emacs-posframe: Update to 1.1.0. * gnu/packages/emacs-xyz.scm (emacs-posframe): Update to 1.1.0. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 9ba178513c..78b98879ad 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -13942,14 +13942,14 @@ methods from a given list.") (define-public emacs-posframe (package (name "emacs-posframe") - (version "1.0.4") + (version "1.1.0") (source (origin (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/" "posframe-" version ".tar")) (sha256 - (base32 "0i2pw90gw9zb22gj8yyvcp3b2k1bxxhbjj0idvr5iz1vd9023bc6")))) + (base32 "0ddm149dz71nksbpz7rwa8cax1nisf6wklv5iq4zrcbf5ghpagkg")))) (build-system emacs-build-system) ;; emacs-minimal does not include the function font-info. (arguments -- cgit 1.4.1 From 395e3ba3dd321783eba2936923532b26968704b1 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 4 Nov 2021 15:28:36 +0100 Subject: gnu: emacs-ivy-posframe: Update to 0.6.3. * gnu/packages/emacs-xyz.scm (emacs-ivy-posframe): Update to 0.6.3. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 78b98879ad..7448786de3 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -27247,14 +27247,14 @@ interface.") (define-public emacs-ivy-posframe (package (name "emacs-ivy-posframe") - (version "0.6.2") + (version "0.6.3") (source (origin (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/" "ivy-posframe-" version ".tar")) (sha256 - (base32 "1x6pm0pry2j7yazhxvq1gydbymwll9yg85m8qi4sh8s0pnm0vjzk")))) + (base32 "0b498qzaydjrhplx4d7zcrs883dlrhfiz812sv4m3pmhfwifcchh")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-ivy" ,emacs-ivy) -- cgit 1.4.1 From b7aff8e6404b916a8908c8055326a4835ae67488 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 4 Nov 2021 16:11:22 +0100 Subject: gnu: parlatype: Update to 3.0. * gnu/packages/gnome.scm (parlatype): Update to 3.0. [homepage]: Update URL. --- gnu/packages/gnome.scm | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index efa000fd87..28d4432334 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -48,7 +48,7 @@ ;;; Copyright © 2020 Oleg Pykhalov ;;; Copyright © 2020 Pierre Neidhardt ;;; Copyright © 2020 raingloom -;;; Copyright © 2020 Nicolas Goaziou +;;; Copyright © 2020, 2021 Nicolas Goaziou ;;; Copyright © 2020 Naga Malleswari ;;; Copyright © 2020 Ryan Prior ;;; Copyright © 2020, 2021 Vinicius Monego @@ -11836,7 +11836,7 @@ provided there is a DBus service present: (define-public parlatype (package (name "parlatype") - (version "2.1") + (version "3.0") (source (origin (method git-fetch) @@ -11845,13 +11845,17 @@ provided there is a DBus service present: (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1c15ja0rwz3jj8bnqdq0nmqka39iwrhy8krdv2a2x8nl4shfpmv0")))) + (base32 "0mvzagkg9kq2ji6mffi37mdjxmlj3wa65d4lcayij9hsmjlklnzs")))) (build-system meson-build-system) (arguments `(#:glib-or-gtk? #t #:tests? #f ;require internet access #:phases (modify-phases %standard-phases + (add-after 'unpack 'skip-gtk-update-icon-cache + (lambda _ + (substitute* "data/meson_post_install.py" + (("gtk-update-icon-cache") "true")))) (add-after 'install 'wrap-parlatype ;; Add gstreamer plugin provided in this package to system's ;; plugins. @@ -11862,8 +11866,7 @@ provided there is a DBus service present: ":" (getenv "GST_PLUGIN_SYSTEM_PATH")))) (wrap-program (string-append out "/bin/parlatype") - `("GST_PLUGIN_SYSTEM_PATH" ":" = (,gst-plugin-path)))) - #t))))) + `("GST_PLUGIN_SYSTEM_PATH" ":" = (,gst-plugin-path))))))))) (native-inputs `(("appstream-glib" ,appstream-glib) ("desktop-file-utils" ,desktop-file-utils) ;for desktop-file-validate @@ -11876,10 +11879,11 @@ provided there is a DBus service present: ("gst-plugins-good" ,gst-plugins-good) ("gstreamer" ,gstreamer) ("gtk+" ,gtk+) + ("iso-codes" ,iso-codes) ("pocketsphinx" ,pocketsphinx) ("pulseaudio" ,pulseaudio) ("sphinxbase" ,sphinxbase))) - (home-page "http://gkarsay.github.io/parlatype/") + (home-page "https://www.parlatype.org") (synopsis "GNOME audio player for transcription") (description "Parlatype is an audio player for the GNOME desktop environment. Its main purpose is the manual transcription of spoken -- cgit 1.4.1 From 0e6a21c0875283f430cf48f6a5073a9ace47c6e5 Mon Sep 17 00:00:00 2001 From: phodina Date: Wed, 13 Oct 2021 22:07:09 +0000 Subject: gnu: Add rust-cpuprofiler-0.0. * gnu/packages/crates-io.scm (rust-cpuprofiler-0.0): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index b229683ab4..d28f12ab84 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -46,6 +46,7 @@ #:use-module (gnu packages admin) #:use-module (gnu packages cmake) #:use-module (gnu packages compression) + #:use-module (gnu packages cpp) #:use-module (gnu packages crates-graphics) #:use-module (gnu packages crates-gtk) #:use-module (gnu packages crypto) @@ -10724,6 +10725,32 @@ to the @code{is_x86_feature_detected!} macro.") to @code{is_x86_feature_detected}.") (license (list license:expat license:asl2.0)))) +(define-public rust-cpuprofiler-0.0 + (package + (name "rust-cpuprofiler") + (version "0.0.4") + (source + (origin + (method url-fetch) + (uri (crate-uri "cpuprofiler" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0az588yyl9r13w4k7xfdh5ckfaq52fwpjry2q2hblazxpjflgy23")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-error-chain" ,rust-error-chain-0.12) + ("rust-lazy-static" ,rust-lazy-static-1) + ("rust-pkg-config" ,rust-pkg-config-0.3)))) + (inputs + `(("gperftools" ,gperftools))) + (home-page "https://github.com/AtheMathmo/cpuprofiler") + (synopsis "Bindings to Google's cpu profiler") + (description "This package provides bindings to Google's cpu profiler.") + (license license:bsd-2))) + (define-public rust-crates-index-0.13 (package (name "rust-crates-index") -- cgit 1.4.1 From 468bb6710f3549076137217d680442ecc2cef0e5 Mon Sep 17 00:00:00 2001 From: phodina Date: Wed, 13 Oct 2021 22:10:36 +0000 Subject: gnu: Add rust-libpulse-sys-1. * gnu/packages/crates-io.scm (rust-libpulse-sys-1): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index d28f12ab84..81b8b596d2 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -64,6 +64,7 @@ #:use-module (gnu packages nettle) #:use-module (gnu packages pcre) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages pulseaudio) #:use-module (gnu packages python) #:use-module (gnu packages rust) #:use-module (gnu packages rust-apps) @@ -26150,6 +26151,39 @@ file. @end itemize") (license license:gpl2+))) + +(define-public rust-libpulse-sys-1 + (package + (name "rust-libpulse-sys") + (version "1.18.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "libpulse-sys" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "10msfr8f951v86ag0fl2bsm4a3siq2r7hz9bqhhg7i234s1yj5yg")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-libc" ,rust-libc-0.2) + ("rust-num-derive" ,rust-num-derive-0.3) + ("rust-num-traits" ,rust-num-traits-0.2) + ("rust-pkg-config" ,rust-pkg-config-0.3) + ("rust-winapi" ,rust-winapi-0.3)))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("pulseaudio" ,pulseaudio))) + (home-page "https://github.com/jnqnfe/pulse-binding-rust") + (synopsis "FFI bindings for the PulseAudio") + (description + "This package provides FFI bindings for the PulseAudio libpulse system +library.") + (license (list license:expat license:asl2.0)))) + (define-public rust-libsqlite3-sys-0.22 (package (name "rust-libsqlite3-sys") -- cgit 1.4.1 From b30e2834f7f3cc16689a31195637f452426ce3d0 Mon Sep 17 00:00:00 2001 From: phodina Date: Wed, 13 Oct 2021 22:11:11 +0000 Subject: gnu: Add rust-libpulse-binding-2. * gnu/packages/crates-io.scm (rust-libpulse-binding-2): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 81b8b596d2..3166f92bee 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -26151,6 +26151,44 @@ file. @end itemize") (license license:gpl2+))) +;; https://github.com/jnqnfe/pulse-binding-rust/blob/c788a8069f455f864d2ba5f0aa5f62e6648dfd26/pulse-sys/build.rs +;; fix location of pulseaudio +(define-public rust-libpulse-binding-2 + (package + (name "rust-libpulse-binding") + (version "2.23.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "libpulse-binding" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1qx85j489mmad9cvw5k71271l3qy4s8a5qq8a9wac6cfi4viz5fv")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-bitflags" ,rust-bitflags-1) + ("rust-libc" ,rust-libc-0.2) + ("rust-libpulse-sys" ,rust-libpulse-sys-1) + ("rust-num-derive" ,rust-num-derive-0.3) + ("rust-num-traits" ,rust-num-traits-0.2) + ("rust-winapi" ,rust-winapi-0.3)) + #:phases + (modify-phases %standard-phases + (add-before 'check 'set-HOME + (lambda _ (setenv "HOME" "/tmp") #t))))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("pulseaudio" ,pulseaudio))) + (home-page "https://github.com/jnqnfe/pulse-binding-rust") + (synopsis "Binding for the PulseAudio libpulse library") + (description + "This package provides a Rust language binding for the PulseAudio libpulse +library.") + (license (list license:expat license:asl2.0)))) (define-public rust-libpulse-sys-1 (package -- cgit 1.4.1 From 575fcd3045ff1649e5319b6701ff9e28e97793e0 Mon Sep 17 00:00:00 2001 From: phodina Date: Wed, 13 Oct 2021 22:11:54 +0000 Subject: gnu: Add i3status-rust. * gnu/packages/rust-apps.scm (i3status-rust): New variable. * gnu/packages/patches/i3status-rust-enable-unstable-features.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Signed-off-by: Efraim Flashner --- .../i3status-rust-enable-unstable-features.patch | 20 ++++++ gnu/packages/rust-apps.scm | 77 ++++++++++++++++++++++ 2 files changed, 97 insertions(+) create mode 100644 gnu/packages/patches/i3status-rust-enable-unstable-features.patch (limited to 'gnu') diff --git a/gnu/packages/patches/i3status-rust-enable-unstable-features.patch b/gnu/packages/patches/i3status-rust-enable-unstable-features.patch new file mode 100644 index 0000000000..535b45d865 --- /dev/null +++ b/gnu/packages/patches/i3status-rust-enable-unstable-features.patch @@ -0,0 +1,20 @@ +From 3006390c0058f06c255d9850327163aebcdc3b40 Mon Sep 17 00:00:00 2001 +From: Petr Hodina +Date: Mon, 11 Oct 2021 22:35:39 +0200 +Subject: [PATCH] Enable unstable features. + + +diff --git a/src/main.rs b/src/main.rs +index d9e964b..820e22e 100644 +--- a/src/main.rs ++++ b/src/main.rs +@@ -1,3 +1,6 @@ ++#![feature(bool_to_option)] ++#![feature(clamp)] ++ + #[macro_use] + mod de; + #[macro_use] +-- +2.33.0 + diff --git a/gnu/packages/rust-apps.scm b/gnu/packages/rust-apps.scm index 27cd57de8b..be60f3f376 100644 --- a/gnu/packages/rust-apps.scm +++ b/gnu/packages/rust-apps.scm @@ -12,6 +12,7 @@ ;;; Copyright © 2021 Zheng Junjie <873216071@qq.com> ;;; Copyright © 2021 Alexandru-Sergiu Marton ;;; Copyright © 2021 Maxim Cournoyer +;;; Copyright © 2021 Petr Hodina ;;; ;;; This file is part of GNU Guix. ;;; @@ -34,6 +35,8 @@ #:use-module (guix download) #:use-module (guix git-download) #:use-module (guix packages) + #:use-module (guix utils) + #:use-module (gnu packages) #:use-module (gnu packages admin) #:use-module (gnu packages compression) #:use-module (gnu packages crates-io) @@ -41,12 +44,14 @@ #:use-module (gnu packages curl) #:use-module (gnu packages documentation) #:use-module (gnu packages fontutils) + #:use-module (gnu packages glib) #:use-module (gnu packages gtk) #:use-module (gnu packages jemalloc) #:use-module (gnu packages linux) #:use-module (gnu packages ssh) #:use-module (gnu packages pcre) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages pulseaudio) #:use-module (gnu packages python-xyz) #:use-module (gnu packages rust) #:use-module (gnu packages tls) @@ -440,6 +445,78 @@ characters, ASCII whitespace characters, other ASCII characters and non-ASCII.") "This package provides a command-line benchmarking tool.") (license (list license:expat license:asl2.0)))) +(define-public i3status-rust + (package + (name "i3status-rust") + (version "0.20.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/greshake/i3status-rust") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (patches (search-patches "i3status-rust-enable-unstable-features.patch")) + (sha256 + (base32 "00gzm3g297s9bfp13vnb623p7dfac3g6cdhz2b3lc6l0kmnnqs1s")))) + (build-system cargo-build-system) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("curl" ,curl) + ("dbus" ,dbus) + ("pulseaudio" ,pulseaudio) + ("openssl" ,openssl) + ("zlib" ,zlib))) + (arguments + `(#:features '("pulseaudio" "libpulse-binding") + #:install-source? #f + #:cargo-inputs + (("rust-chrono" ,rust-chrono-0.4) + ("rust-chrono-tz" ,rust-chrono-tz-0.5) + ("rust-crossbeam-channel" ,rust-crossbeam-channel-0.5) + ("rust-curl" ,rust-curl-0.4) + ("rust-dbus" ,rust-dbus-0.9) + ("rust-dbus-tree" ,rust-dbus-tree-0.9) + ("rust-lazy-static" ,rust-lazy-static-1) + ("rust-nix" ,rust-nix-0.20) + ("rust-nl80211" ,rust-nl80211-0.0.2) + ("rust-serde" ,rust-serde-1) + ("rust-serde-derive" ,rust-serde-derive-1) + ("rust-serde-json" ,rust-serde-json-1) + ("rust-signal-hook" ,rust-signal-hook-0.3) + ("rust-swayipc" ,rust-swayipc-2) + ("rust-toml" ,rust-toml-0.5) + ("rust-cpuprofiler" ,rust-cpuprofiler-0.0) + ("rust-inotify" ,rust-inotify-0.9) + ("rust-libpulse-binding" ,rust-libpulse-binding-2) + ("rust-maildir" ,rust-maildir-0.5) + ("rust-notmuch" ,rust-notmuch-0.6) + ("rust-progress" ,rust-progress-0.2)) + #:cargo-development-inputs + (("rust-assert-fs" ,rust-assert-fs-1)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-resources-path + (lambda* (#:key outputs #:allow-other-keys) + (let ((resources (string-append %output "/share"))) + (substitute* "src/util.rs" + (("/usr/share/i3status-rust") resources))))) + (add-after 'install 'install-resources + (lambda* (#:key outputs #:allow-other-keys) + (copy-recursively "files" (string-append %output "/share")))) + (add-after 'unpack 'enable-unstable-features + (lambda _ + (setenv "RUSTC_BOOTSTRAP" "1") + #t))))) + (home-page "https://github.com/greshake/i3status-rust") + (synopsis "i3status, written in pure Rust") + (description "@code{i3status-rs} is a feature-rich and resource-friendly +replacement for i3status, written in pure Rust. It provides a way to display +@code{blocks} of system information (time, battery status, volume, etc) on the i3 +bar. It is also compatible with sway.") + (license license:gpl3))) + (define-public ripgrep (package (name "ripgrep") -- cgit 1.4.1 From 1ffc0a6be3c1613b2d99ceea098174d1f11f6f3f Mon Sep 17 00:00:00 2001 From: Kyle Meyer Date: Thu, 4 Nov 2021 23:24:08 -0400 Subject: gnu: git-annex: Update to 8.20211028. * gnu/packages/haskell-apps.scm (git-annex): Update to 8.20211028. Signed-off-by: Efraim Flashner --- gnu/packages/haskell-apps.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/haskell-apps.scm b/gnu/packages/haskell-apps.scm index 994214e900..faa3b52c5c 100644 --- a/gnu/packages/haskell-apps.scm +++ b/gnu/packages/haskell-apps.scm @@ -316,14 +316,14 @@ to @code{cabal repl}).") (define-public git-annex (package (name "git-annex") - (version "8.20211011") + (version "8.20211028") (source (origin (method url-fetch) (uri (string-append "https://hackage.haskell.org/package/" "git-annex/git-annex-" version ".tar.gz")) (sha256 - (base32 "02s7921ihmbndp7lk1nhhiljky02ikq4qax4mhg609qjhbl6piwd")))) + (base32 "0bff1bchp60hbslb9yaagvd7hym26w0c3gkkssm7sildwqazwpng")))) (build-system haskell-build-system) (arguments `(#:configure-flags -- cgit 1.4.1 From 3827c66dc1d9760f6f7f4753a518124075f10e64 Mon Sep 17 00:00:00 2001 From: Vagrant Cascadian Date: Fri, 5 Nov 2021 11:21:12 -0700 Subject: gnu: diffoscope: Update to 190. * gnu/packages/diffoscope.scm (diffoscope): Update to 190. [arguments]: Remove 'skip-python-tests phase. --- gnu/packages/diffoscope.scm | 11 ++--------- 1 file changed, 2 insertions(+), 9 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/diffoscope.scm b/gnu/packages/diffoscope.scm index 5a227d059e..3f5928d23b 100644 --- a/gnu/packages/diffoscope.scm +++ b/gnu/packages/diffoscope.scm @@ -73,7 +73,7 @@ (define-public diffoscope (package (name "diffoscope") - (version "189") + (version "190") (source (origin (method git-fetch) @@ -82,7 +82,7 @@ (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0dai9gwsr9xnficjy8myq6xr301y4iy82aidm936qsqjwrp8q1sm")) + (base32 "10q93qybwqf2nzj3iakw1pxhccq10ixm9fn7xgdr4p88qb0wchb5")) (patches (search-patches "diffoscope-fix-llvm-test.patch")))) (build-system python-build-system) @@ -109,13 +109,6 @@ (string-append "['" (which "stat") "',")) (("\\['getfacl',") (string-append "['" (which "getfacl") "',"))))) - (add-after 'unpack 'skip-python-tests - (lambda _ - ;; Python tests appear to assume python 3.9, remove - ;; phase when python is upgraded - (substitute* "tests/comparators/test_python.py" - (("def test_identification") - "def skip_test_identification")))) (add-after 'build 'build-man-page (lambda* (#:key (make-flags '()) #:allow-other-keys) (apply invoke "make" "-C" "doc" make-flags))) -- cgit 1.4.1 From 90ab3ef812341b6f031e4724a56c0d7663977be9 Mon Sep 17 00:00:00 2001 From: phodina Date: Fri, 5 Nov 2021 05:48:58 +0000 Subject: gnu: Add lowdown. * gnu/packages/markup.scm (lowdown): New variable. Signed-off-by: Liliana Marie Prikler --- gnu/packages/markup.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/markup.scm b/gnu/packages/markup.scm index 368976bfde..40b7a3d8c6 100644 --- a/gnu/packages/markup.scm +++ b/gnu/packages/markup.scm @@ -7,6 +7,8 @@ ;;; Copyright © 2020 Marius Bakke ;;; Copyright © 2020 EuAndreh ;;; Copyright © 2021 Noisytoot +;;; Copyright © 2021 Zhu Zihao +;;; Copyright © 2021 Petr Hodina ;;; ;;; This file is part of GNU Guix. ;;; @@ -25,6 +27,7 @@ (define-module (gnu packages markup) #:use-module (guix licenses) + #:use-module ((guix licenses) #:prefix license:) #:use-module (guix download) #:use-module (guix git-download) #:use-module (guix packages) @@ -34,6 +37,7 @@ #:use-module (guix build-system perl) #:use-module (guix build-system python) #:use-module (guix utils) + #:use-module (gnu packages base) #:use-module (gnu packages compression) #:use-module (gnu packages) #:use-module (gnu packages perl) @@ -114,6 +118,36 @@ convert it to structurally valid XHTML (or HTML).") (license (non-copyleft "file://License.text" "See License.text in the distribution.")))) +(define-public lowdown + (package + (name "lowdown") + (version "0.10.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://kristaps.bsd.lv/lowdown/snapshots/lowdown-" + version ".tar.gz")) + (sha256 + (base32 "15v2kk4ffqw3n6y6n9plch4qcib3ynnhw0ih8wn2v9qgn4jssp5p")))) + (build-system gnu-build-system) + (arguments + `(#:test-target "regress" + #:phases + (modify-phases %standard-phases + (replace 'configure + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (invoke "./configure" + (string-append "PREFIX=" out) + (string-append "MANDIR=" out "/share/man")))))))) + (native-inputs + `(("which" ,which))) + (home-page "https://kristaps.bsd.lv/lowdown/") + (synopsis "Simple Markdown translator") + (description "Lowdown is a Markdown translator producing HTML5, +roff documents in the ms and man formats, LaTeX, gemini, and terminal output.") + (license license:isc))) + (define-public discount (package (name "discount") -- cgit 1.4.1 From 43cb6aa4a0898ebd160ed6ca61daf8440eaebc63 Mon Sep 17 00:00:00 2001 From: phodina Date: Fri, 5 Nov 2021 05:49:55 +0000 Subject: gnu: Use license: prefix. * gnu/packages/markup.scm (hoedown, markdown, discount, perl-text-markdown-discount, cmark, smu, md4c, python-mistletoe) [license]: Prefix with license:. Signed-off-by: Liliana Marie Prikler --- gnu/packages/markup.scm | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/markup.scm b/gnu/packages/markup.scm index 40b7a3d8c6..06e653a1c9 100644 --- a/gnu/packages/markup.scm +++ b/gnu/packages/markup.scm @@ -26,7 +26,6 @@ ;;; along with GNU Guix. If not, see . (define-module (gnu packages markup) - #:use-module (guix licenses) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix download) #:use-module (guix git-download) @@ -71,7 +70,7 @@ (description "Hoedown is a standards compliant, fast, secure markdown processing library written in C.") (home-page "https://github.com/hoedown/hoedown") - (license expat))) + (license license:expat))) (define-public markdown (package @@ -115,8 +114,8 @@ processing library written in C.") "Markdown is a text-to-HTML conversion tool for web writers. It allows you to write using an easy-to-read, easy-to-write plain text format, then convert it to structurally valid XHTML (or HTML).") - (license (non-copyleft "file://License.text" - "See License.text in the distribution.")))) + (license (license:non-copyleft "file://License.text" + "See License.text in the distribution.")))) (define-public lowdown (package @@ -192,7 +191,7 @@ roff documents in the ms and man formats, LaTeX, gemini, and terminal output.") "Discount is a markdown implementation, written in C. It provides a @command{markdown} command, and a library.") (home-page "https://www.pell.portland.or.us/~orc/Code/discount/") - (license bsd-3))) + (license license:bsd-3))) (define-public perl-text-markdown-discount (package @@ -237,7 +236,7 @@ implementation. use Text::Markdown::Discount; my $html = markdown($text) @end example") - (license perl-license))) + (license license:perl-license))) (define-public cmark (package @@ -277,7 +276,7 @@ for parsing and rendering CommonMark.") ;; cmark is distributed with a BSD-2 license, but some components are Expat ;; licensed. The CommonMark specification is Creative Commons CC-BY-SA 4.0 ;; licensed. See 'COPYING' in the source distribution for more information. - (license (list bsd-2 expat cc-by-sa4.0)))) + (license (list license:bsd-2 license:expat license:cc-by-sa4.0)))) (define-public smu (package @@ -313,7 +312,7 @@ amount of indents it scales just great. Smu was started as a rewrite of Markdown but became something more lightweight and consistent. The biggest difference between Markdown and smu is that smu doesn't support reference style links.") - (license x11))) + (license license:x11))) (define-public md4c (package @@ -335,7 +334,7 @@ and smu is that smu doesn't support reference style links.") (description "MD4C is a C Markdown parser with a SAX-like interface. It is compliant to the CommonMark specification, with a few extensions.") - (license expat))) + (license license:expat))) (define-public python-mistletoe (package @@ -357,4 +356,4 @@ parser that supports definitions of custom tokens. Parsing Markdown into an abstract syntax tree also allows @code{mistletoe} to swap out renderers for different output formats, without touching any of the core components.") - (license expat))) + (license license:expat))) -- cgit 1.4.1 From c55a64cb7e82e88e26c26995f983fc9675b6276e Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Fri, 5 Nov 2021 23:12:31 +0100 Subject: gnu: opam: Update to 2.1.1. * gnu/packages/ocaml.scm (opam): Update to 2.1.1. --- gnu/packages/ocaml.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 660bc44bc7..b04ca1d287 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -776,7 +776,7 @@ the opam file format.") (define-public opam (package (name "opam") - (version "2.1.0") + (version "2.1.1") (source (origin (method git-fetch) (uri (git-reference @@ -785,7 +785,7 @@ the opam file format.") (file-name (git-file-name name version)) (sha256 (base32 - "12l7l4pbzy71k1yc7ym5aczajszvc9bqkdnfg8xhqc8ch8j1h1lj")))) + "12cxpnkv8n90g66b31c7hsxl2yy537fgf19xhr6zn4n024bh6dh3")))) (build-system dune-build-system) (arguments `(#:test-target "." -- cgit 1.4.1 From 4fd12fb00d595b6f6a5d5cc734863f4c4bc5f46c Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Fri, 5 Nov 2021 15:31:34 -0400 Subject: gnu: webkitgtk: Fix build on i686-linux. Fixes . * gnu/packages/webkit.scm (webkitgtk)[arguments]: Use quasiquote for the argument list. When building on i686-linux, insert a 'substitute*' form in the 'prepare-build-environment' phase that disables the use of '__builtin_mul_overflow'. --- gnu/packages/webkit.scm | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/webkit.scm b/gnu/packages/webkit.scm index e54b680855..a184cc9b32 100644 --- a/gnu/packages/webkit.scm +++ b/gnu/packages/webkit.scm @@ -241,7 +241,7 @@ acceleration in mind, leveraging common 3D graphics APIs for best performance.") (build-system cmake-build-system) (outputs '("out" "doc")) (arguments - '(#:tests? #f ; no tests + `(#:tests? #f ; no tests #:build-type "Release" ; turn off debugging symbols to save space #:configure-flags (list "-DPORT=GTK" @@ -299,6 +299,13 @@ acceleration in mind, leveraging common 3D graphics APIs for best performance.") (lambda* (#:key inputs #:allow-other-keys) (setenv "CC" "clang") (setenv "CXX" "clang++") + ;; XXX Until we switch back to using GCC, + ;; work around . + ,@(if (string=? "i686-linux" (%current-system)) + '((substitute* "Source/WTF/wtf/CheckedArithmetic.h" + (("#define USE_MUL_OVERFLOW 1") + "#define USE_MUL_OVERFLOW 0"))) + '()) #t)) (add-after 'install 'move-doc-files (lambda* (#:key outputs #:allow-other-keys) -- cgit 1.4.1 From af14c6f10135ac92ea760ca4d57109a75b6d575e Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 6 Nov 2021 10:19:31 +0100 Subject: gnu: emacs-git-modes: Update to 1.4.0. * gnu/packages/emacs-xyz.scm (emacs-git-modes): Update to 1.4.0. --- gnu/packages/emacs-xyz.scm | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 7448786de3..44999f8aba 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -651,16 +651,16 @@ some utility functions, and commands using that infrastructure.") (define-public git-modes (package (name "emacs-git-modes") - (version "1.3.0") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/magit/git-modes") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0m8qfjj5hzxwyyi34sbk11qz5fix6z80hiki0v0a838sq4f586b6")))) + (version "1.4.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/magit/git-modes") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0aqz65pcqc35h5z4s606f48iqn87h5v9nj3cp6n9yjxa2v7w5hfk")))) (build-system emacs-build-system) (home-page "https://github.com/magit/git-modes") (synopsis "Emacs major modes for Git configuration files") -- cgit 1.4.1 From 3c3131b1c51fda96e574887eba34dc2b1e8f4966 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 6 Nov 2021 10:20:15 +0100 Subject: gnu: emacs-git-modes: Add TeXinfo markup to description. * gnu/packages/emacs-xyz.scm (git-modes): Add TeXinfo markup. --- gnu/packages/emacs-xyz.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 44999f8aba..d3901af675 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -666,7 +666,8 @@ some utility functions, and commands using that infrastructure.") (synopsis "Emacs major modes for Git configuration files") (description "This package provides Emacs major modes for editing various Git -configuration files, such as .gitattributes, .gitignore, and .git/config.") +configuration files, such as @file{.gitattributes}, @file{.gitignore}, and +@file{.git/config}.") (license license:gpl3+))) (define-public emacs-with-editor -- cgit 1.4.1 From d82fd7c2dd542693988f61fb15c020e3209ac7ec Mon Sep 17 00:00:00 2001 From: Liliana Marie Prikler Date: Sat, 6 Nov 2021 09:21:02 +0100 Subject: gnu: webkitgtk: Disable SSE2 when not on x86_64. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/webkit.scm (webkitgtk)[#:phases]: Add ‘disable-sse2’ if the current (target) system is not an x86_64 one. --- gnu/packages/webkit.scm | 7 +++++++ 1 file changed, 7 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/webkit.scm b/gnu/packages/webkit.scm index a184cc9b32..5931402b98 100644 --- a/gnu/packages/webkit.scm +++ b/gnu/packages/webkit.scm @@ -295,6 +295,13 @@ acceleration in mind, leveraging common 3D graphics APIs for best performance.") (("libWPEBackend-fdo-([\\.0-9]+)\\.so" all version) (string-append wpebackend-fdo "/lib/" all))) #t))) + ,@(if (string-prefix? "x86_64" (or (%current-target-system) + (%current-system))) + '() + '((add-after 'unpack 'disable-sse2 + (lambda _ + (substitute* "Source/cmake/DetectSSE2.cmake" + (("CHECK_FOR_SSE2\\(\\)") "")))))) (add-before 'configure 'prepare-build-environment (lambda* (#:key inputs #:allow-other-keys) (setenv "CC" "clang") -- cgit 1.4.1 From 36d1f71440162388e7901234875298bf947c3679 Mon Sep 17 00:00:00 2001 From: phodina Date: Thu, 4 Nov 2021 21:34:11 +0000 Subject: gnu: Add emacs-ntlm. * gnu/packages/emacs-xyz.scm (emacs-ntlm): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index d3901af675..feca4feb31 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -47,6 +47,7 @@ ;;; Copyright © 2019 mikadoZero ;;; Copyright © 2019 Gabriel Hondet ;;; Copyright © 2019, 2020, 2021 Joseph LaFreniere +;;; Copyright © 2019 Todor Kondić 15669 ;;; Copyright © 2019 Amar Singh ;;; Copyright © 2019 Baptiste Strazzulla ;;; Copyright © 2019 Giacomo Leidi @@ -25658,6 +25659,24 @@ provided. Those alternative commands are and bound by default to their corresponding Evil keys.") (license license:expat)))) +(define-public emacs-ntlm + (package + (name "emacs-ntlm") + (version "2.1.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://elpa.gnu.org/packages/ntlm-" version ".el")) + (sha256 + (base32 "01d0bcmh8a36qf871w6bc05kjk9bmnh843m9869xw06zyvqwg9mv")))) + (build-system emacs-build-system) + (home-page "https://elpa.gnu.org/packages/ntlm.html") + (synopsis "NTLM (NT LanManager) authentication support") + (description + "This library is a direct translation of the Samba release 2.2.0 +implementation of Windows NT and LanManager compatible password encryption.") + (license license:gpl3+))) + (define-public emacs-evil-traces (let ((commit "1931e3ea2c64b4aec393a9c25063c330deff55e3") (revision "2")) -- cgit 1.4.1 From dfb74165178630d5481f8a21c158c314625069e4 Mon Sep 17 00:00:00 2001 From: phodina Date: Thu, 4 Nov 2021 21:35:26 +0000 Subject: gnu: Add emacs-nadvice. * gnu/packages/emacs-xyz.scm (emacs-nadvice): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index feca4feb31..ef05531b2c 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -25677,6 +25677,26 @@ corresponding Evil keys.") implementation of Windows NT and LanManager compatible password encryption.") (license license:gpl3+))) +(define-public emacs-nadvice + (package + (name "emacs-nadvice") + (version "0.3") + (source + (origin + (method url-fetch) + (uri (string-append "https://elpa.gnu.org/packages/" + "nadvice-" version ".el")) + (sha256 + (base32 "0gi3csnxbs8h7iy0scsl35sic3gv90swa89hhdjwb7qvpirfdcgw")))) + (build-system emacs-build-system) + (home-page "https://elpa.gnu.org/packages/nadvice.html") + (synopsis "Forward compatibility for Emacs-24.4's nadvice") + (description + "This package tries to re-implement some of nadvice.el's functionality on +top of the old defadvice system, to help users of defadvice move to the new +advice system without dropping support for Emacs<24.4.") + (license license:gpl3+))) + (define-public emacs-evil-traces (let ((commit "1931e3ea2c64b4aec393a9c25063c330deff55e3") (revision "2")) -- cgit 1.4.1 From 68abfea5c28d7e1749341360fb0283a77d823690 Mon Sep 17 00:00:00 2001 From: phodina Date: Thu, 4 Nov 2021 21:35:56 +0000 Subject: gnu: Add emacs-url-http-ntlm. * gnu/packages/emacs-xyz.scm (emacs-url-http-ntlm): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index ef05531b2c..c8e6a3f221 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -25697,6 +25697,24 @@ top of the old defadvice system, to help users of defadvice move to the new advice system without dropping support for Emacs<24.4.") (license license:gpl3+))) +(define-public emacs-url-http-ntlm + (package + (name "emacs-url-http-ntlm") + (version "2.0.4") + (source + (origin + (method url-fetch) + (uri (string-append "https://elpa.gnu.org/packages/" + "url-http-ntlm-" version ".el")) + (sha256 + (base32 "1cakq2ykraci7d1gl8rnpv4f2f5ffyaidhqb1282g7i72adwmb98")))) + (build-system emacs-build-system) + (propagated-inputs `(("emacs-ntlm" ,emacs-ntlm))) + (home-page "https://elpa.gnu.org/packages/url-http-ntlm.html") + (synopsis "NTLM authentication for the url library") + (description "This package provides a NTLM handler for the URL package.") + (license license:gpl3+))) + (define-public emacs-evil-traces (let ((commit "1931e3ea2c64b4aec393a9c25063c330deff55e3") (revision "2")) -- cgit 1.4.1 From 2a66d806a85000c72472ff521a26fea8d77cce83 Mon Sep 17 00:00:00 2001 From: phodina Date: Thu, 4 Nov 2021 21:36:27 +0000 Subject: gnu: Add emacs-soap-client. * gnu/packages/emacs-xyz.scm (emacs-soap-client): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index c8e6a3f221..bd53ce00da 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -25715,6 +25715,24 @@ advice system without dropping support for Emacs<24.4.") (description "This package provides a NTLM handler for the URL package.") (license license:gpl3+))) +(define-public emacs-soap-client + (package + (name "emacs-soap-client") + (version "3.2.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://elpa.gnu.org/packages/" + "soap-client-" version ".tar")) + (sha256 + (base32 "1s0bwnip22nj6kgjadd4zlj9j729hiyyjb66sr51i2mddnf9i95s")))) + (build-system emacs-build-system) + (home-page "httpa://elpa.gnu.org/packages/soap-client.html") + (synopsis "Access SOAP web services") + (description + "This package provides a SOAP client to access web services.") + (license license:gpl3+))) + (define-public emacs-evil-traces (let ((commit "1931e3ea2c64b4aec393a9c25063c330deff55e3") (revision "2")) -- cgit 1.4.1 From d101486d7fb2a81ecd570fb826a29d98757649ed Mon Sep 17 00:00:00 2001 From: phodina Date: Thu, 4 Nov 2021 21:36:58 +0000 Subject: gnu: Add emacs-fsm. * gnu/packages/emacs-xyz.scm (emacs-fsm): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index bd53ce00da..f44ae42206 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -25733,6 +25733,24 @@ advice system without dropping support for Emacs<24.4.") "This package provides a SOAP client to access web services.") (license license:gpl3+))) +(define-public emacs-fsm + (package + (name "emacs-fsm") + (version "0.2.1") + (source + (origin + (method url-fetch) + (uri (string-append "https://elpa.gnu.org/packages/fsm-" version ".el")) + (sha256 + (base32 "1jyxyqdbfl8nv7c50q0sg3w5p7whp1sqgi7w921k5hfar4d11qqp")))) + (build-system emacs-build-system) + (home-page "https://elpa.gnu.org/packages/fsm.html") + (synopsis "Finite State Machine library") + (description + "This package provides Finite State Machine library to make asynchronous +programming in Emacs Lisp easy and fun.") + (license license:gpl3+))) + (define-public emacs-evil-traces (let ((commit "1931e3ea2c64b4aec393a9c25063c330deff55e3") (revision "2")) -- cgit 1.4.1 From c161ec6dc59293249f7ff2fc04a6b1ae49ae8f5b Mon Sep 17 00:00:00 2001 From: phodina Date: Thu, 4 Nov 2021 21:37:39 +0000 Subject: gnu: Add emacs-excorporate. * gnu/packages/emacs-xyz.scm (emacs-excorporate): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index f44ae42206..07d85b968f 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -25751,6 +25751,28 @@ advice system without dropping support for Emacs<24.4.") programming in Emacs Lisp easy and fun.") (license license:gpl3+))) +(define-public emacs-excorporate + (package + (name "emacs-excorporate") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://elpa.gnu.org/packages/" + "excorporate-" version ".tar")) + (sha256 + (base32 "1g0wc2kp15ra323b4rxvdh58q9c4h7m20grw6a0cs53m7l9xi62f")))) + (build-system emacs-build-system) + (propagated-inputs + `(("emacs-fsm" ,emacs-fsm) + ("emacs-nadvice" ,emacs-nadvice) + ("emacs-soap-client" ,emacs-soap-client) + ("emacs-url-http-ntlm" ,emacs-url-http-ntlm))) + (home-page "https://elpa.gnu.org/packages/excorporate.html") + (synopsis "Exchange integration") + (description "This package provides Exchange integration for Emacs.") + (license license:gpl3+))) + (define-public emacs-evil-traces (let ((commit "1931e3ea2c64b4aec393a9c25063c330deff55e3") (revision "2")) -- cgit 1.4.1 From 39bf4eb38fe827dbfe0b86a1f0ee6953efd502f1 Mon Sep 17 00:00:00 2001 From: Aleksandr Vityazev Date: Fri, 5 Nov 2021 14:45:24 +0000 Subject: gnu: Add emacs-devdocs. * gnu/packages/emacs-xyz.scm (emacs-devdocs): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 07d85b968f..86271cb392 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -25183,6 +25183,27 @@ Dash docsets.") through Dash docsets.") (license license:expat)))) +(define-public emacs-devdocs + (package + (name "emacs-devdocs") + (version "0.2") + (source + (origin + (method url-fetch) + (uri (string-append + "https://elpa.gnu.org/packages/" + "devdocs-" version ".tar")) + (sha256 + (base32 "1npc7yra7pvf86ahmz1h7hnjxrz15ar1vjcalg4ilizypycpgrwj")))) + (build-system emacs-build-system) + (home-page "https://github.com/astoff/devdocs.el") + (synopsis "Emacs viewer for DevDocs") + (description + "This package provides a documentation viewer similar to Emacs's +built-in Info browser, but geared towards documentation obtained from +@url{https://devdocs.io}.") + (license license:gpl3+))) + (define-public emacs-cascading-dir-locals (let ((release "0.1") (revision "0") -- cgit 1.4.1 From e58994f113e9acc063943ce9d6340b1301e1346a Mon Sep 17 00:00:00 2001 From: Xinglu Chen Date: Fri, 5 Nov 2021 18:15:34 +0100 Subject: gnu: msmtp: Update to 1.8.19. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/mail.scm (msmtp): Update to 1.8.19. [properties]: Set ‘release-monitoring-url’. --- gnu/packages/mail.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index ca748bff1b..6a9a69c410 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -1734,14 +1734,14 @@ addons which can add many functionalities to the base client.") (define-public msmtp (package (name "msmtp") - (version "1.8.18") + (version "1.8.19") (source (origin (method url-fetch) (uri (string-append "https://marlam.de/msmtp/releases/" "/msmtp-" version ".tar.xz")) (sha256 - (base32 "19b0anfrkg4lqp4h13qi2rqgwvipp1ga0id237nwbp7b6ypn5z0l")))) + (base32 "0ssj8izcw1fywihlip6wljd9i41w23cy0vp69sz4v1vn26cf389l")))) (build-system gnu-build-system) (inputs `(("libsecret" ,libsecret) @@ -1772,6 +1772,8 @@ addons which can add many functionalities to the base client.") ;; connection, instead look up and ping debian.org. (substitute* (string-append bin "/msmtpq") (("EMAIL_CONN_TEST=n") "EMAIL_CONN_TEST=p")))))))) + (properties + '((release-monitoring-url . "https://marlam.de/msmtp/download/"))) (synopsis "Simple and easy to use SMTP client with decent sendmail compatibility") (description -- cgit 1.4.1 From 567c4f4495fd1681bc6bd1ca3e9d1a87e120ac61 Mon Sep 17 00:00:00 2001 From: Liliana Marie Prikler Date: Sat, 6 Nov 2021 16:00:24 +0100 Subject: Update mailmap and copyright assignments for Liliana Marie Prikler. Use full names everywhere. * .mailmap: Use full name for Liliana Marie Prikler. * gnu/packages/zig.scm: Likewise. --- .mailmap | 3 ++- gnu/packages/zig.scm | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/.mailmap b/.mailmap index 072673e5a0..3e18831d0a 100644 --- a/.mailmap +++ b/.mailmap @@ -41,7 +41,8 @@ Joshua Grant Joshua Grant Kei Kebreau Leo Famulari -Liliana Prikler Leo Prikler +Liliana Marie Prikler +Liliana Marie Prikler Leo Prikler Ludovic Courtès Marek Benc Marius Bakke diff --git a/gnu/packages/zig.scm b/gnu/packages/zig.scm index ab62f554f4..a7966736e8 100644 --- a/gnu/packages/zig.scm +++ b/gnu/packages/zig.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2021 Liliana Prikler +;;; Copyright © 2021 Liliana Marie Prikler ;;; Copyright © 2021 Sarah Morgensen ;;; ;;; This file is part of GNU Guix. -- cgit 1.4.1 From 5e7c2eb7ae95064cb0c68e2ca6a9256a3b9f0b0d Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 5 Nov 2021 23:56:36 +0100 Subject: gnu: fio: Don't bother wrapping scripts. fio comes with many scripts of varying utility. Some require extra additional programs, which users can easily install as needed; there is little use in imposing all optional dependencies on all users of fio. * gnu/packages/benchmark.scm (fio)[arguments]: Remove patch-paths phase. Rewrite move-outputs to move all discovered scripts and not wrap any. [inputs]: Remove GNUPLOT, PYTHON-2, PYTHON2-NUMPY, and PYTHON2-PANDAS. Add PYTHON. --- gnu/packages/benchmark.scm | 48 ++++++++++++++++------------------------------ 1 file changed, 16 insertions(+), 32 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/benchmark.scm b/gnu/packages/benchmark.scm index a422073805..3cee5dae17 100644 --- a/gnu/packages/benchmark.scm +++ b/gnu/packages/benchmark.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016, 2017 Marius Bakke +;;; Copyright © 2016, 2017, 2021 Marius Bakke ;;; Copyright © 2017 Dave Love ;;; Copyright © 2018–2021 Tobias Geerinckx-Rice ;;; Copyright © 2018, 2019 Ricardo Wurmus @@ -63,22 +63,11 @@ "0ba9cnjrnm3nwcfbhh5x2sycr54j3yn1rqn76kjdyz40f3pdg3qm")))) (build-system gnu-build-system) (arguments - '(#:test-target "test" + `(#:modules (,@%gnu-build-system-modules + (ice-9 textual-ports)) + #:test-target "test" #:phases (modify-phases %standard-phases - (add-after - 'unpack 'patch-paths - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out")) - (gnuplot (string-append (assoc-ref inputs "gnuplot") - "/bin/gnuplot"))) - (substitute* "tools/plot/fio2gnuplot" - (("/usr/share/fio") (string-append out "/share/fio")) - ;; FIXME (upstream): The 'gnuplot' executable is used inline - ;; in various os.system() calls mixed with *.gnuplot filenames. - (("; do gnuplot") (string-append "; do " gnuplot)) - (("gnuplot mymath") (string-append gnuplot " mymath")) - (("gnuplot mygraph") (string-append gnuplot " mygraph")))))) (replace 'configure (lambda* (#:key outputs #:allow-other-keys) ;; The configure script doesn't understand some of the @@ -87,32 +76,27 @@ (invoke "./configure" (string-append "--prefix=" out))))) ;; The main `fio` executable is fairly small and self contained. - ;; Moving the auxiliary python and gnuplot scripts to a separate - ;; output saves almost 400 MiB on the closure. + ;; Moving the auxiliary scripts to a separate output saves ~100 MiB + ;; on the closure. (add-after 'install 'move-outputs (lambda* (#:key outputs #:allow-other-keys) (let ((oldbin (string-append (assoc-ref outputs "out") "/bin")) - (newbin (string-append (assoc-ref outputs "utils") "/bin"))) + (newbin (string-append (assoc-ref outputs "utils") "/bin")) + (script? (lambda* (file #:rest _) + (call-with-input-file file + (lambda (port) + (char=? #\# (peek-char port))))))) (mkdir-p newbin) (for-each (lambda (file) - (let ((src (string-append oldbin "/" file)) - (dst (string-append newbin "/" file))) - (link src dst) - (delete-file src))) - '("fio2gnuplot" "fiologparser_hist.py" - "fiologparser.py")) - ;; Make sure numpy et.al is found. - (wrap-program (string-append newbin "/fiologparser_hist.py") - `("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH")))))))))) + (link file (string-append newbin "/" (basename file))) + (delete-file file)) + (find-files oldbin script?)))))))) (outputs '("out" "utils")) (inputs `(("ceph" ,ceph "lib") ("libaio" ,libaio) - ("gnuplot" ,gnuplot) - ("zlib" ,zlib) - ("python-numpy" ,python2-numpy) - ("python-pandas" ,python2-pandas) - ("python" ,python-2))) + ("python" ,python) + ("zlib" ,zlib))) (home-page "https://github.com/axboe/fio") (synopsis "Flexible I/O tester") (description -- cgit 1.4.1 From 75f2eb41ccd21fd38dc371830d93fc63083a83b4 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 6 Nov 2021 00:03:39 +0100 Subject: gnu: fio: Disable Ceph/RADOS support. This little-used feature is easy to add on demand and blows up the closure. * gnu/packages/benchmark.scm (fio)[inputs]: Remove CEPH. --- gnu/packages/benchmark.scm | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/benchmark.scm b/gnu/packages/benchmark.scm index 3cee5dae17..e355a47d4e 100644 --- a/gnu/packages/benchmark.scm +++ b/gnu/packages/benchmark.scm @@ -47,7 +47,6 @@ #:use-module (gnu packages python-science) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) - #:use-module (gnu packages storage) #:use-module (ice-9 match)) (define-public fio @@ -93,8 +92,7 @@ (find-files oldbin script?)))))))) (outputs '("out" "utils")) (inputs - `(("ceph" ,ceph "lib") - ("libaio" ,libaio) + `(("libaio" ,libaio) ("python" ,python) ("zlib" ,zlib))) (home-page "https://github.com/axboe/fio") -- cgit 1.4.1 From 290a7664b58d2a018096c6388ae3468eb4cd88ec Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 6 Nov 2021 00:09:30 +0100 Subject: gnu: fio: Disable native CPU compiler optimizations. * gnu/packages/benchmark.scm (fio)[arguments]: Add #:configure-flags. Adjust configure phase accordingly. --- gnu/packages/benchmark.scm | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/benchmark.scm b/gnu/packages/benchmark.scm index e355a47d4e..9741814c82 100644 --- a/gnu/packages/benchmark.scm +++ b/gnu/packages/benchmark.scm @@ -65,15 +65,17 @@ `(#:modules (,@%gnu-build-system-modules (ice-9 textual-ports)) #:test-target "test" + #:configure-flags '("--disable-native") ;don't generate code for the build CPU #:phases (modify-phases %standard-phases (replace 'configure - (lambda* (#:key outputs #:allow-other-keys) + (lambda* (#:key (configure-flags ''()) outputs #:allow-other-keys) ;; The configure script doesn't understand some of the - ;; GNU options, so we can't use #:configure-flags. + ;; GNU options, so we can't use the stock phase. (let ((out (assoc-ref outputs "out"))) - (invoke "./configure" - (string-append "--prefix=" out))))) + (apply invoke "./configure" + (string-append "--prefix=" out) + configure-flags)))) ;; The main `fio` executable is fairly small and self contained. ;; Moving the auxiliary scripts to a separate output saves ~100 MiB ;; on the closure. -- cgit 1.4.1 From 9c306695511245d3c42df6c7203131e2d99d6527 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 6 Nov 2021 22:15:36 +0100 Subject: gnu: Add emacs-citar. * gnu/packages/emacs-xyz.scm (emacs-citar): New variable. --- gnu/packages/emacs-xyz.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 86271cb392..9cc8c5d6e2 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -17755,6 +17755,42 @@ and publications from various sources, by keywords or by DOI. References are automatically fetched from well-curated sources, and formatted as BibTeX.") (license license:gpl3+))) +(define-public emacs-citar + (package + (name "emacs-citar") + (version "0.8") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/bdarcus/citar") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1jrfcfr976c9nb2vpfrh6yhck5gm34wcjzbk0m6gq2xg3qfv2g6p")))) + (build-system emacs-build-system) + (propagated-inputs + `(("emacs-auctex" ,emacs-auctex) + ("emacs-helm-bibtex" ,emacs-helm-bibtex) + ("emacs-org" ,emacs-org) + ("emacs-parsebib" ,emacs-parsebib) + ("emacs-s" ,emacs-s))) + (home-page "https://github.com/bdarcus/citar") + (synopsis "Emacs package to quickly find and act on bibliographic entries") + (description + "This package provides a completing-read front-end to browse and +act on BibTeX, BibLaTeX, and CSL JSON bibliographic data, and LaTeX, +markdown, and Org cite editing support. + +When used with Vertico (or Selectrum), Embark, and Marginalia, it +provides similar functionality to helm-bibtex and ivy-bibtex: quick +filtering and selecting of bibliographic entries from the minibuffer, +and the option to run different commands against them. + +With Embark, it also makes available at-point actions in Org +citations.") + (license license:gpl3+))) + (define-public emacs-helm-bibtex (let ((commit "d4471232be26793fbf56c0ac3690b5f537c378b9") (revision "2")) -- cgit 1.4.1 From b2ee0798eede3dfa5551a8e9f4e8459b42da6140 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 6 Nov 2021 22:42:55 +0100 Subject: gnu: emacs-helm-bibtex: Update to 2.0.0-3.aa77534. * gnu/packages/emacs-xyz.scm (emacs-helm-bibtex): Update to 2.0.0-3.aa77534. --- gnu/packages/emacs-xyz.scm | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 9cc8c5d6e2..620e9cda47 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -17792,12 +17792,11 @@ citations.") (license license:gpl3+))) (define-public emacs-helm-bibtex - (let ((commit "d4471232be26793fbf56c0ac3690b5f537c378b9") - (revision "2")) + (let ((commit "aa775340ba691d2322948bfdc6a88158568a1399") + (revision "3")) (package (name "emacs-helm-bibtex") - (version (string-append "2.0.0" "-" revision "." - (string-take commit 7))) + (version (git-version "2.0.0" revision commit)) (source (origin (method git-fetch) @@ -17806,8 +17805,7 @@ citations.") (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 - "1bkzhic6qckb267025il1r3xcpz99kisphxiafni1pxvf9jafr0j")))) + (base32 "1d3mc17ga09m41i06khghlvixr6gsiacifnhdbrfnp0w5592aprk")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-helm" ,emacs-helm) -- cgit 1.4.1 From b96ae47bb08f315be8c22f0ee4248dc36c0d6d29 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sun, 7 Nov 2021 00:20:35 +0100 Subject: gnu: emacs-geiser-guile: Update to 0.18. * gnu/packages/emacs-xyz.scm (emacs-geiser-guile): Update to 0.18. [arguments]<#:phases>: Remove trailing #t from phase. --- gnu/packages/emacs-xyz.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 620e9cda47..98e429cbb0 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -281,7 +281,7 @@ e.g. emacs-geiser-guile for Guile.") (define-public emacs-geiser-guile (package (name "emacs-geiser-guile") - (version "0.17") + (version "0.18") (source (origin (method git-fetch) @@ -290,7 +290,7 @@ e.g. emacs-geiser-guile for Guile.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0iw23nlgqppf6f00ly50m8lq85n9mv244pw3whxv0hynfjxr2ic0")))) + (base32 "0gndf0w8dbv54bzc04svp2ck8wypa7i3b8kpixf6rkg91l79xpci")))) (build-system emacs-build-system) (arguments '(#:include (cons "^src/" %default-include) @@ -305,8 +305,7 @@ e.g. emacs-geiser-guile for Guile.") ;; loaded, so let's defer that until it is. (("\\(geiser-activate-implementation .*\\)" all) (string-append - "(eval-after-load 'geiser-impl '" all ")"))) - #t))))) + "(eval-after-load 'geiser-impl '" all ")")))))))) (inputs `(("guile" ,guile-2.2))) (propagated-inputs -- cgit 1.4.1 From b11badfb4cd8124f2f467697cf2a4d15e7f20b19 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Sat, 6 Nov 2021 05:31:04 -0400 Subject: gnu: webkitgtk: Improve the 32-bit x86 target check. * gnu/packages/webkit.scm (webkitgtk)[arguments]: In the 'prepare-build-environment' phase, use 'target-x86-32?'. --- gnu/packages/webkit.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/webkit.scm b/gnu/packages/webkit.scm index 5931402b98..688e745d95 100644 --- a/gnu/packages/webkit.scm +++ b/gnu/packages/webkit.scm @@ -308,7 +308,7 @@ acceleration in mind, leveraging common 3D graphics APIs for best performance.") (setenv "CXX" "clang++") ;; XXX Until we switch back to using GCC, ;; work around . - ,@(if (string=? "i686-linux" (%current-system)) + ,@(if (target-x86-32?) '((substitute* "Source/WTF/wtf/CheckedArithmetic.h" (("#define USE_MUL_OVERFLOW 1") "#define USE_MUL_OVERFLOW 0"))) -- cgit 1.4.1 From b217208dd03fbaae5805015f45d916ded1858689 Mon Sep 17 00:00:00 2001 From: Felix Gruber Date: Sat, 6 Nov 2021 13:53:53 +0000 Subject: gnu: libosmium: Update to 2.17.1. * gnu/packages/geo.scm (libosmium): Update to 2.17.1. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/geo.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index f460e08828..18e8a455c6 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -1192,7 +1192,7 @@ to create databases that are optimized for rendering/tile/map-services.") (define-public libosmium (package (name "libosmium") - (version "2.15.6") + (version "2.17.1") (source (origin (method git-fetch) @@ -1201,7 +1201,7 @@ to create databases that are optimized for rendering/tile/map-services.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0rqy18bbakp41f44y5id9ixh0ar2dby46z17p4115z8k1vv9znq2")))) + (base32 "0xw71lrw4q4sdm51rl0zg87ywxfkxbw9h52zqim0z0xl5qh5q8xf")))) (build-system cmake-build-system) (propagated-inputs `(("boost" ,boost) -- cgit 1.4.1 From 53bbbfb77c699fbaa0678f6274737a62f1d91243 Mon Sep 17 00:00:00 2001 From: Felix Gruber Date: Sat, 6 Nov 2021 13:54:11 +0000 Subject: gnu: protozero: Update to 1.7.0. * gnu/packages/protobuf.scm (protozero): Update to 1.7.0. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/protobuf.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/protobuf.scm b/gnu/packages/protobuf.scm index 322ce61b13..27f4f83f83 100644 --- a/gnu/packages/protobuf.scm +++ b/gnu/packages/protobuf.scm @@ -7,6 +7,7 @@ ;;; Copyright © 2020, 2021 Maxim Cournoyer ;;; Copyright © 2020 Vinicius Monego ;;; Copyright © 2020 Brett Gilio +;;; Copyright © 2021 Felix Gruber ;;; ;;; This file is part of GNU Guix. ;;; @@ -209,7 +210,7 @@ code.") (define-public protozero (package (name "protozero") - (version "1.6.8") + (version "1.7.0") (source (origin (method git-fetch) @@ -218,7 +219,7 @@ code.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1hfijpfylf1c71wa3mk70gjc88b6k1q7cxb87cwqdflw5q2x8ma6")))) + (base32 "0fdihfl5j68wayjjxvpvhvnjq1anzcfnfl09f68wpzbkg3zmhblz")))) (build-system cmake-build-system) (home-page "https://github.com/mapbox/protozero") (synopsis "Minimalistic protocol buffer decoder and encoder in C++") -- cgit 1.4.1 From dc8e9d6f88de01db1ded39a8ca699bc988522a72 Mon Sep 17 00:00:00 2001 From: Felix Gruber Date: Sat, 6 Nov 2021 13:54:21 +0000 Subject: gnu: osm2pgsql: Update to 1.5.1. * gnu/packages/geo.scm (osm2pgsql): Update to 1.5.1. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/geo.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index 18e8a455c6..adfec13b4f 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -1225,7 +1225,7 @@ OpenStreetMap data.") (define-public osm2pgsql (package (name "osm2pgsql") - (version "1.2.2") + (version "1.5.1") (source (origin (method git-fetch) @@ -1234,7 +1234,7 @@ OpenStreetMap data.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1j35aa8qinhavliqi5pdm0viyi7lm5xyk402rliaxxs1r2hbsafn")) + (base32 "0i18mskcs087dn3f3h9n7j0wafn8502m0h13mrjwin38xsz0crfj")) (modules '((guix build utils))) (snippet '(begin -- cgit 1.4.1 From a0f1476e8fa20e80c71f83342b82338ddedbf7fd Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 7 Nov 2021 14:16:38 +0100 Subject: gnu: emacs-stream: Don't set a source file name. This is a follow-up to 678248f5ea3d3d19bc2a5a41d90bb30e63e667e1. * gnu/packages/emacs-xyz.scm (emacs-stream)[source]: Remove FILE-NAME, as the tarball name is already OK; and the -checkout name breaks build system assumptions on the core-updates branch. --- gnu/packages/emacs-xyz.scm | 1 - 1 file changed, 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 98e429cbb0..17638cc801 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -12665,7 +12665,6 @@ editing nginx config files.") (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/" "stream-" version ".tar")) - (file-name (git-file-name name version)) (sha256 (base32 "00c3n4gyxzv7vczqms0d62kl8zsmjfyxa92mwxn2snyx857a9jfw")))) (build-system emacs-build-system) -- cgit 1.4.1 From 6f4541841687b8d96e1518ed6ab6241434a140f5 Mon Sep 17 00:00:00 2001 From: Thorsten Wilms Date: Sun, 7 Nov 2021 12:03:15 +0100 Subject: gnu: x42-plugins: Update to 20211016. * gnu/packages/music.scm (x42-plugins): Update to 20211016. Signed-off-by: Efraim Flashner --- gnu/packages/music.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 1156c8eece..21b85d2ec0 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -6076,7 +6076,7 @@ short-time Fourier transform, available as LV2 audio plugin and JACK client.") (define-public x42-plugins (package (name "x42-plugins") - (version "20200714") + (version "20211016") (source (origin (method url-fetch) @@ -6084,7 +6084,7 @@ short-time Fourier transform, available as LV2 audio plugin and JACK client.") (string-append "https://gareus.org/misc/x42-plugins/x42-plugins-" version ".tar.xz")) (sha256 - (base32 "1av05ykph8x67018hm9zfgh1vk0zi39mvrsxkj6bm4hkarxf0vvl")))) + (base32 "11bf6q42ihyk4qxwf83y0847zzyl65kwpbk3hmyz0f0ykil5fsb7")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no "check" target -- cgit 1.4.1 From 3e6f857354854277cc9169e88c19cef75cdd883c Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 7 Nov 2021 22:25:23 +0200 Subject: gnu: x42-plugins: Prepare for cross-compiling. * gnu/packages/music.scm (x42-plugins)[arguments]: Remove 'set-CC-variable phase. Use cc-for-target in make-flags. --- gnu/packages/music.scm | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 21b85d2ec0..32ed4081b6 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -6093,13 +6093,10 @@ short-time Fourier transform, available as LV2 audio plugin and JACK client.") "LIBZITACONVOLVER=-lzita-convolver" (string-append "FONTFILE=" (assoc-ref %build-inputs "font-dejavu") - "/share/fonts/truetype/DejaVuSans-Bold.ttf")) + "/share/fonts/truetype/DejaVuSans-Bold.ttf") + (string-append "CC=" ,(cc-for-target))) #:phases (modify-phases %standard-phases - (add-before 'build 'set-CC-variable - (lambda _ - (setenv "CC" "gcc") - #t)) (delete 'configure)))) (inputs `(("cairo" ,cairo) -- cgit 1.4.1 From 9bf3bc841820c7cdb389a4a472c12678e9cb5857 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sun, 7 Nov 2021 14:15:23 +0000 Subject: gnu: Add rust-color-backtrace-0.5. * gnu/packages/crates-io.scm (rust-color-backtrace-0.5): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 3166f92bee..bdf5627c0c 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -9306,6 +9306,30 @@ diagnostics easy and relatively painless for everyone!") ("rust-structopt" ,rust-structopt-0.3) ("rust-unindent" ,rust-unindent-0.1)))))) +(define-public rust-color-backtrace-0.5 + (package + (name "rust-color-backtrace") + (version "0.5.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "color-backtrace" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "11fn3snykx90w3nznzrcf4r164zmhk790asx0kzryf4r7i308v6d")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-atty" ,rust-atty-0.2) + ("rust-backtrace" ,rust-backtrace-0.3) + ("rust-regex" ,rust-regex-1) + ("rust-termcolor" ,rust-termcolor-1)))) + (home-page "https://github.com/athre0z/color-backtrace") + (synopsis "Colorful panic backtraces") + (description "This package provides colorful panic backtraces.") + (license (list license:expat license:asl2.0)))) + (define-public rust-color-quant-1 (package (name "rust-color-quant") -- cgit 1.4.1 From cd968c83aa4911f41e5d25c753dcea99098a26ce Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sun, 7 Nov 2021 14:15:24 +0000 Subject: gnu: Add rust-xmltree-0.10. * gnu/packages/crates-io.scm (rust-xmltree-0.10): New variable. (rust-xmltree-0.8): Inherit from above. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 52 ++++++++++++++++++++++++++++++---------------- 1 file changed, 34 insertions(+), 18 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index bdf5627c0c..d79bc8676d 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -60655,31 +60655,47 @@ formatters with per-field documentation generated for each structure. configuration file and/or environment variables.") (license (list license:expat license:asl2.0)))) -(define-public rust-xmltree-0.8 +(define-public rust-xmltree-0.10 (package (name "rust-xmltree") - (version "0.8.0") + (version "0.10.3") (source - (origin - (method url-fetch) - (uri (crate-uri "xmltree" version)) - (file-name - (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "0w0y0jz7lhxg05ca6ngfj0lj8sbrjh4vaqv13q7qaqkhs7lsx3pz")))) + (origin + (method url-fetch) + (uri (crate-uri "xmltree" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1jqzwhr1a5cknflsshhhjlllmd1xi04qdkjsls2bnmv5mxgagn6p")))) (build-system cargo-build-system) (arguments - `(#:cargo-inputs - (("rust-indexmap" ,rust-indexmap-1) - ("rust-xml-rs" ,rust-xml-rs-0.7)))) - (home-page #f) - (synopsis - "Parse an XML file into a simple tree-like structure") - (description - "Parse an XML file into a simple tree-like structure") + `(#:cargo-inputs + (("rust-indexmap" ,rust-indexmap-1) + ("rust-xml-rs" ,rust-xml-rs-0.8)))) + (home-page "https://github.com/eminence/xmltree-rs") + (synopsis "Parse an XML file into a simple tree-like structure") + (description "This package provides a small library for parsing an XML +file into an in-memory tree structure.") (license license:expat))) +(define-public rust-xmltree-0.8 + (package + (inherit rust-xmltree-0.10) + (name "rust-xmltree") + (version "0.8.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "xmltree" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0w0y0jz7lhxg05ca6ngfj0lj8sbrjh4vaqv13q7qaqkhs7lsx3pz")))) + (arguments + `(#:cargo-inputs + (("rust-indexmap" ,rust-indexmap-1) + ("rust-xml-rs" ,rust-xml-rs-0.7)))))) + (define-public rust-svd-parser-0.9 (package (name "rust-svd-parser") -- cgit 1.4.1 From 551e39ccb1a4a7449aee08fb178a3929e7e47406 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sun, 7 Nov 2021 14:15:25 +0000 Subject: gnu: Add rust-snake-case-0.3. * gnu/packages/crates-io.scm (rust-snake-case-0.3): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index d79bc8676d..b583e8b8aa 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -47844,6 +47844,29 @@ More importantly, this library also provides the ability to un-escape a given escaped text to recover the original string.") (license license:gpl3))) +(define-public rust-snake-case-0.3 + (package + (name "rust-snake-case") + (version "0.3.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "snake-case" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1v4f132rk9wxiw8hb3kgnixirzr8kbfhg2lgsf4b85vbg02a0jfn")))) + (build-system cargo-build-system) + (arguments + `(#:rust ,rust-1.52 ; fix for E0658 + #:cargo-inputs (("rust-serde" ,rust-serde-1)))) + (home-page "https://github.com/emilk/snake_case") + (synopsis "String-like type that only contains non-empty snake_case") + (description + "This package provides a String-like type that can only contain valid +non-empty snake_case.") + (license license:expat))) + (define-public rust-snap-1 (package (name "rust-snap") -- cgit 1.4.1 From 38912f139ff08569ce7d1806ee055de104cd0879 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sun, 7 Nov 2021 14:15:26 +0000 Subject: gnu: Add rust-diffus-derive-0.10. * gnu/packages/crates-io.scm (rust-diffus-derive-0.10): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index b583e8b8aa..ee513a345f 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -14362,6 +14362,30 @@ common subsequence. The diff algorithms include Myer's diff and Patience diff.") (license (list license:asl2.0 license:expat)))) +(define-public rust-diffus-derive-0.10 + (package + (name "rust-diffus-derive") + (version "0.10.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "diffus-derive" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1a7sgbzhqa7gk3xhvkci91myc86gkwxs04vfxbl8f64y7l1jsfmr")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-proc-macro2" ,rust-proc-macro2-1) + ("rust-quote" ,rust-quote-1) + ("rust-syn" ,rust-syn-1)))) + (home-page "https://github.com/distil/diffus") + (synopsis "Diff two instances of any data structure") + (description "This package finds the difference between two instances of +any data structure. Supports derive on structs and enums.") + (license license:asl2.0))) + (define-public rust-digest-0.9 (package (name "rust-digest") -- cgit 1.4.1 From e9eb6b1102061dd987d85ed9a76449e4dc44ff7c Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sun, 7 Nov 2021 14:15:27 +0000 Subject: gnu: Add rust-diffus-0.10. * gnu/packages/crates-io.scm (rust-diffus-0.10): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index ee513a345f..1853409b61 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -14362,6 +14362,35 @@ common subsequence. The diff algorithms include Myer's diff and Patience diff.") (license (list license:asl2.0 license:expat)))) +(define-public rust-diffus-0.10 + (package + (name "rust-diffus") + (version "0.10.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "diffus" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0lsn5h1mfa8x7bfg9yqgr52p7drigpwgm5q8qh4r07dmfd5g43rw")))) + (build-system cargo-build-system) + (arguments + `(#:rust ,rust-1.52 ; fix for E0658 + #:cargo-inputs + (("rust-diffus-derive" ,rust-diffus-derive-0.10) + ("rust-indexmap" ,rust-indexmap-1) + ("rust-itertools" ,rust-itertools-0.10) + ("rust-serde" ,rust-serde-1) + ("rust-snake-case" ,rust-snake-case-0.3) + ("rust-uuid" ,rust-uuid-0.8)))) + (home-page "https://github.com/distil/diffus") + (synopsis "Diff two instances of any data structure") + (description "This package finds the difference between two instances of +any data structure. It supports: collections, Strings, Maps etc. Uses LC +where applicable. Also supports derive via `diffus-derive`.") + (license license:asl2.0))) + (define-public rust-diffus-derive-0.10 (package (name "rust-diffus-derive") -- cgit 1.4.1 From b76b29957ebb059a9b39075218726293ac24f3b1 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sun, 7 Nov 2021 14:15:28 +0000 Subject: gnu: Add rust-log-mdc-0.1. * gnu/packages/crates-io.scm (rust-log-mdc-0.1): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 1853409b61..a73f7e9f60 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -26960,6 +26960,25 @@ by inspecting the system for user preference.") `(#:cargo-inputs (("rust-log" ,rust-log-0.4)))))) +(define-public rust-log-mdc-0.1 + (package + (name "rust-log-mdc") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "log-mdc" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1iw1x3qhjvrac35spikn5h06a1rxd9vw216jk8h52jhz9i0j2kd9")))) + (build-system cargo-build-system) + (home-page "https://github.com/sfackler/rust-log-mdc") + (synopsis "Mapped diagnostic context (MDC) for use with the `log` crate") + (description "This package provides a mapped diagnostic context (MDC) for +use with the `log` crate.") + (license (list license:expat license:asl2.0)))) + (define-public rust-logtest-2 (package (name "rust-logtest") -- cgit 1.4.1 From 6e3eba9d1f87d7fa0f7c13e0d22096da31295a32 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sun, 7 Nov 2021 14:15:29 +0000 Subject: gnu: Add rust-log4rs-1. * gnu/packages/crates-io.scm (rust-log4rs-1): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 49 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index a73f7e9f60..4ccf463e23 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -26979,6 +26979,55 @@ by inspecting the system for user preference.") use with the `log` crate.") (license (list license:expat license:asl2.0)))) +(define-public rust-log4rs-1 + (package + (name "rust-log4rs") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "log4rs" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "04d21kkb6if7hly0syp64m15a9695fpfgvlnff3gy58i1n42lmyi")))) + (build-system cargo-build-system) + (arguments + `(#:tests? #f ; 37 passed, 1 failed + #:cargo-inputs + (("rust-anyhow" ,rust-anyhow-1) + ("rust-arc-swap" ,rust-arc-swap-0.4) + ("rust-chrono" ,rust-chrono-0.4) + ("rust-derivative" ,rust-derivative-2) + ("rust-flate2" ,rust-flate2-1) + ("rust-fnv" ,rust-fnv-1) + ("rust-humantime" ,rust-humantime-2) + ("rust-libc" ,rust-libc-0.2) + ("rust-log" ,rust-log-0.4) + ("rust-log-mdc" ,rust-log-mdc-0.1) + ("rust-parking-lot" ,rust-parking-lot-0.11) + ("rust-regex" ,rust-regex-1) + ("rust-serde" ,rust-serde-1) + ("rust-serde-value" ,rust-serde-value-0.7) + ("rust-serde-json" ,rust-serde-json-1) + ("rust-serde-yaml" ,rust-serde-yaml-0.8) + ("rust-thiserror" ,rust-thiserror-1) + ("rust-thread-id" ,rust-thread-id-3) + ("rust-toml" ,rust-toml-0.5) + ("rust-typemap" ,rust-typemap-0.3) + ("rust-winapi" ,rust-winapi-0.3)) + #:cargo-development-inputs + (("rust-humantime" ,rust-humantime-2) + ("rust-lazy-static" ,rust-lazy-static-1) + ("rust-streaming-stats" + ,rust-streaming-stats-0.2) + ("rust-tempfile" ,rust-tempfile-3)))) + (home-page "https://github.com/estk/log4rs") + (synopsis "Highly configurable logging implementation") + (description "This package provides a highly configurable multi-output +logging implementation for the `log` facade.") + (license (list license:expat license:asl2.0)))) + (define-public rust-logtest-2 (package (name "rust-logtest") -- cgit 1.4.1 From 73679a6837416644aa51c6d39e7970fa57d5aef1 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Sun, 31 Oct 2021 01:55:12 +0530 Subject: gnu: Add python-webcolors. * gnu/packages/python-web.scm (python-webcolors): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/python-web.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index a37681dab4..6887944d21 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -44,6 +44,7 @@ ;;; Copyright © 2021 Greg Hogan ;;; Copyright © 2021 Maxime Devos ;;; Copyright © 2021 Pradana Aumars +;;; Copyright © 2021 Arun Isaac ;;; ;;; This file is part of GNU Guix. ;;; @@ -6252,6 +6253,43 @@ comments, or tags from HTML snippets, extract base url from HTML snippets, translate entities on HTML strings, among other things.") (license license:bsd-3))) +(define-public python-webcolors + (package + (name "python-webcolors") + (version "1.11.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "webcolors" version)) + (sha256 + (base32 "1rkda75h2p65zx6r84c9mjavn4xpviqvqrklvdvcklapd5in1wvn")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? inputs outputs #:allow-other-keys) + (when tests? + (add-installed-pythonpath inputs outputs) + (invoke "pytest"))))))) + (native-inputs + `(("python-pytest" ,python-pytest))) + (home-page "https://github.com/ubernostrum/webcolors") + (synopsis "HTML/CSS color definitions library") + (description "@code{python-webcolors} is a module for working with +HTML/CSS color definitions. Normalizing and converting between the following +formats is supported. +@itemize +@item Specification-defined color names +@item Six-digit hexadecimal +@item Three-digit hexadecimal +@item Integer rgb() triplet +@item Percentage rgb() triplet +@end itemize +Only the RGB colorspace is supported. Conversion to/from the HSL colorspace +can be handled by the @code{colorsys} module in the Python standard library.") + (license license:bsd-3))) + (define-public python-flask-combo-jsonapi (package (name "python-flask-combo-jsonapi") -- cgit 1.4.1 From 7ebed0cdc8043852bed7f5ca639f16bac30cc124 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Sun, 31 Oct 2021 01:55:13 +0530 Subject: gnu: Add weechat-matrix. * gnu/packages/messaging.scm (weechat-matrix): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/messaging.scm | 69 +++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 68 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm index f591078920..ee9bbc71fd 100644 --- a/gnu/packages/messaging.scm +++ b/gnu/packages/messaging.scm @@ -9,7 +9,7 @@ ;;; Copyright © 2016 Andy Patterson ;;; Copyright © 2016, 2017, 2018, 2019 Clément Lassieur ;;; Copyright © 2017 Mekeor Melire -;;; Copyright © 2017, 2018, 2020 Arun Isaac +;;; Copyright © 2017, 2018, 2020, 2021 Arun Isaac ;;; Copyright © 2017–2021 Tobias Geerinckx-Rice ;;; Copyright © 2017 Theodoros Foradis ;;; Copyright © 2017, 2018, 2019 Rutger Helling @@ -2986,4 +2986,71 @@ API. Mattermost is not required.") (home-page "https://github.com/42wim/matterbridge") (license license:asl2.0))) +(define-public weechat-matrix + (package + (name "weechat-matrix") + (version "0.3.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/poljar/weechat-matrix") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1iv55n4k05139f7jzkhczgw4qp6qwilrvfsy3c6v2m1kxffj12d3")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (delete 'build) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((weechat-python (string-append (assoc-ref outputs "out") + "/share/weechat/python"))) + ;; Avoid circular import by renaming the matrix module to + ;; weechat_matrix. + (substitute* (cons "main.py" + (append (find-files "matrix") + (find-files "tests"))) + (("from matrix") "from weechat_matrix") + (("import matrix") "import weechat_matrix")) + ;; Install python modules. + (invoke "make" "install-lib" + (string-append "INSTALLDIR=" + (site-packages inputs outputs) + "/weechat_matrix")) + ;; Extend PYTHONPATH to find installed python modules. + (add-installed-pythonpath inputs outputs) + ;; Augment sys.path so that dependencies are found. + (substitute* "main.py" + (("import os\n" all) + (apply string-append + all + "import sys\n" + (map (lambda (path) + (string-append "sys.path.append('" path "')\n")) + (string-split (getenv "PYTHONPATH") #\:))))) + ;; Install script. + (mkdir-p weechat-python) + (copy-file "main.py" + (string-append weechat-python "/matrix.py"))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest"))))))) + (inputs + `(("python-matrix-nio" ,python-matrix-nio) + ("python-pygments" ,python-pygments) + ("python-pyopenssl" ,python-pyopenssl) + ("python-webcolors" ,python-webcolors))) + (native-inputs + `(("python-pytest" ,python-pytest))) + (home-page "https://github.com/poljar/weechat-matrix") + (synopsis "Weechat Matrix protocol script") + (description "@code{weechat-matrix} is a Python plugin for Weechat that lets +Weechat communicate over the Matrix protocol.") + (license license:isc))) + ;;; messaging.scm ends here -- cgit 1.4.1 From 2ebadb390e0798f39b597a7fb02a1926958a1c24 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Sun, 31 Oct 2021 01:55:14 +0530 Subject: gnu: Add weechat-wee-slack. * gnu/packages/messaging.scm (weechat-wee-slack): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/messaging.scm | 50 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm index ee9bbc71fd..bdd0c29593 100644 --- a/gnu/packages/messaging.scm +++ b/gnu/packages/messaging.scm @@ -3053,4 +3053,54 @@ API. Mattermost is not required.") Weechat communicate over the Matrix protocol.") (license license:isc))) +(define-public weechat-wee-slack + (package + (name "weechat-wee-slack") + (version "2.8.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/wee-slack/wee-slack") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0xfklr0gsc9jgxfyrrb2j756lclz9g8imcb0pk0xgyj8mhsw23zk")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (delete 'build) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; Augment sys.path so that dependencies are found. + (substitute* "wee_slack.py" + (("import sys\n" all) + (apply string-append + all + (map (lambda (path) + (string-append "sys.path.append('" path "')\n")) + (string-split (getenv "PYTHONPATH") #\:))))) + ;; Install script. + (install-file "wee_slack.py" + (string-append (assoc-ref outputs "out") + "/share/weechat/python")))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest"))))))) + (inputs + `(("python-websocket-client" ,python-websocket-client))) + (native-inputs + `(("python-pytest" ,python-pytest))) + (home-page "https://github.com/wee-slack/wee-slack") + (synopsis "Weechat Slack script") + (description "@code{weechat-wee-slack} is a WeeChat native client for +Slack. It provides supplemental features only available in the web/mobile +clients such as synchronizing read markers, typing notification, threads (and +more)! It connects via the Slack API, and maintains a persistent websocket +for notification of events.") + (license license:expat))) + ;;; messaging.scm ends here -- cgit 1.4.1 From b6bb7720eb887fa4497a34611e963ebc90f6a396 Mon Sep 17 00:00:00 2001 From: Felix Gruber Date: Sat, 6 Nov 2021 10:40:36 +0000 Subject: gnu: openttd-engine: Update to 12.0. * gnu/packages/games.scm (openttd-engine): Update engine to 12.0. Signed-off-by: Liliana Marie Prikler --- gnu/packages/games.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index eb3db37c46..70207c6205 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -4287,14 +4287,14 @@ world}, @uref{http://evolonline.org, Evol Online} and (define openttd-engine (package (name "openttd-engine") - (version "1.11.2") + (version "12.0") (source (origin (method url-fetch) (uri (string-append "https://cdn.openttd.org/openttd-releases/" version "/openttd-" version "-source.tar.xz")) (sha256 (base32 - "0v9f93lsdcv3ia28y8iihx9nj9zp6fpf5hkdrpl4ypw159d97fhg")))) + "1p1j5cf4ry57dcgm7qx2g2s00z1c6qgjabb4kqjp00yz00wgv85v")))) (build-system cmake-build-system) (inputs `(("allegro" ,allegro) -- cgit 1.4.1 From c2759211fcc37e1a6cde904217a185e1a6097405 Mon Sep 17 00:00:00 2001 From: Felix Gruber Date: Sat, 6 Nov 2021 10:40:37 +0000 Subject: gnu: openttd-opengfx: Update to 7.1. * packages/games.scm (openttd-opengfx): Update to 7.1. [native-inputs]: Replace python-2 with python. [arguments]: Use cc-for-target. Signed-off-by: Liliana Marie Prikler --- gnu/packages/games.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 70207c6205..bcce16c91c 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -4324,7 +4324,7 @@ engine. When you start it you will be prompted to download a graphics set.") (define openttd-opengfx (package (name "openttd-opengfx") - (version "0.6.1") + (version "7.1") (source (origin (method url-fetch) @@ -4332,10 +4332,10 @@ engine. When you start it you will be prompted to download a graphics set.") version "/opengfx-" version "-source.tar.xz")) (sha256 (base32 - "0jgy8xv7r72m127qn09vr3rxhnbakl2990f7lldsk0d5d8n993vd")))) + "0nhzlk6s73qvznm5fdwcs1b42g2plf26s5ag39fvck45zm7m48jk")))) (build-system gnu-build-system) (arguments - '(#:make-flags (list "CC=gcc" + `(#:make-flags (list (string-append "CC=" ,(cc-for-target)) (string-append "INSTALL_DIR=" (assoc-ref %outputs "out") "/share/games/openttd/baseset/opengfx")) @@ -4363,7 +4363,7 @@ engine. When you start it you will be prompted to download a graphics set.") ("grfcodec" ,grfcodec) ("nml" ,nml) ("which" ,which) - ("python" ,python-2))) + ("python" ,python))) (home-page "http://dev.openttdcoop.org/projects/opengfx") (synopsis "Base graphics set for OpenTTD") (description -- cgit 1.4.1 From 574f4b7d3f8cf934d747dc15a6766c7f764404c7 Mon Sep 17 00:00:00 2001 From: Felix Gruber Date: Sat, 6 Nov 2021 10:40:38 +0000 Subject: gnu: openttd-opensfx: Update to 1.0.2. * packages/games.scm (openttd-opensfx): Update to 1.0.2. [native-inputs]: Replace python-2 with python. Signed-off-by: Liliana Marie Prikler --- gnu/packages/games.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index bcce16c91c..4764021f73 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -4383,7 +4383,7 @@ OpenGFX provides you with... (define openttd-opensfx (package (name "openttd-opensfx") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) @@ -4392,11 +4392,11 @@ OpenGFX provides you with... version "/opensfx-" version "-source.tar.xz")) (sha256 (base32 - "06vycppqcxbfdqlxzna5xr303zgcmpcvj6ylw5b2ws0ssph2f1s0")))) + "0aym026lg0r7dp3jxxs9c0rj8lwy1fz3v9hmk3mml6sycsg3fv42")))) (build-system gnu-build-system) (native-inputs `(("catcodec" ,catcodec) - ("python" ,python-2) + ("python" ,python) ("tar" ,tar))) (arguments `(#:make-flags -- cgit 1.4.1 From c9b991985814b58542e41e375d5fb5d009f55bfc Mon Sep 17 00:00:00 2001 From: Felix Gruber Date: Sun, 7 Nov 2021 20:11:29 +0000 Subject: gnu: openttd-openmsx: Update to 0.4.2. * packages/games.scm (openttd-openmsx): Update to 0.4.2. [native-inputs]: Replace python-2 with python-wrapper. Signed-off-by: Liliana Marie Prikler --- gnu/packages/games.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 4764021f73..0b4f8c6bfe 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -4433,7 +4433,7 @@ the original Transport Tycoon Deluxe.") (define openttd-openmsx (package (name "openttd-openmsx") - (version "0.4.0") + (version "0.4.2") (source (origin (method url-fetch) @@ -4442,11 +4442,13 @@ the original Transport Tycoon Deluxe.") version "/openmsx-" version "-source.tar.xz")) (sha256 (base32 - "0prjljsdgdxqdhhcriqskqha004ybs575xcjq80zha3pqnmrdk0k")))) + "0h583d8fxy78kc3jvpp78r76a48qhxrhm4q7jbnj74aw0kwrcl8g")))) (build-system gnu-build-system) (native-inputs `(("grfcodec" ,grfcodec) - ("python" ,python-2) + ; Scripts are Python3 compatible, but call the interpreter as + ; python instead of python3. + ("python" ,python-wrapper) ("tar" ,tar))) (arguments `(#:make-flags -- cgit 1.4.1 From 92af2ec5d07b124c67f45e0e9d0e1202ac3e2220 Mon Sep 17 00:00:00 2001 From: Felix Gruber Date: Sat, 6 Nov 2021 10:40:40 +0000 Subject: gnu: openttd: Fix build failure. * packages/games.scm (openttd)[native-inputs]: Use gcc-9 to fix build failure. Signed-off-by: Liliana Marie Prikler --- gnu/packages/games.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 0b4f8c6bfe..1e5f0a1e9a 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -4497,6 +4497,7 @@ Transport Tycoon Deluxe.") `(("opengfx" ,openttd-opengfx) ("openmsx" ,openttd-openmsx) ("opensfx" ,openttd-opensfx) + ("gcc" ,gcc-9) ; for #include ,@(package-native-inputs openttd-engine))))) (define openrct2-title-sequences -- cgit 1.4.1 From 153d9bca7231ae0e7d19ac090e5c53ff588b388a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 7 Nov 2021 18:17:47 +0100 Subject: gnu: dvdisaster: Update to 0.79.9. * gnu/packages/cdrom.scm (dvdisaster): Update to 0.79.9. [source, home-page]: Update home page. [arguments]: Don't explicitly return #t from phases. --- gnu/packages/cdrom.scm | 17 ++++++----------- 1 file changed, 6 insertions(+), 11 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cdrom.scm b/gnu/packages/cdrom.scm index 66a259f261..3a7e7b0e3b 100644 --- a/gnu/packages/cdrom.scm +++ b/gnu/packages/cdrom.scm @@ -419,16 +419,14 @@ or @command{xorrisofs} to create ISO 9660 images.") (define-public dvdisaster (package (name "dvdisaster") - (version "0.79.5") + (version "0.79.9") (source (origin (method url-fetch) - ;; Update this (and update HOME-PAGE) when/if one reappears. - (uri (string-append "https://web.archive.org/web/20180428070843/" - "http://dvdisaster.net/downloads/dvdisaster-" + (uri (string-append "https://dvdisaster.jcea.es/downloads/dvdisaster-" version ".tar.bz2")) (sha256 - (base32 "0f8gjnia2fxcbmhl8b3qkr5b7idl8m855dw7xw2fnmbqwvcm6k4w")))) + (base32 "1hz3fvqfdrwb7dn6ggqkpcgyjag37ivm1layw27ncjz9glklxjbr")))) (build-system gnu-build-system) (inputs `(("gtk+" ,gtk+-2))) @@ -447,8 +445,7 @@ or @command{xorrisofs} to create ISO 9660 images.") (with-directory-excursion "regtest" (substitute* "common.bash" (("ISODIR=/var/tmp/regtest") "ISODIR=/tmp")) - (for-each invoke (find-files "." "rs.*\\.bash"))) - #t)) + (for-each invoke (find-files "." "rs.*\\.bash"))))) (add-after 'install 'install-desktop (lambda* (#:key outputs #:allow-other-keys) (let* ((datadir (string-append (assoc-ref outputs "out") "/share"))) @@ -468,10 +465,8 @@ or @command{xorrisofs} to create ISO 9660 images.") (find-files "contrib" "dvdisaster[0-9]*\\.png")) (mkdir-p (string-append datadir "/pixmaps")) (copy-file "contrib/dvdisaster48.xpm" - (string-append datadir "/pixmaps/dvdisaster.xpm")) - #t)))))) - (home-page (string-append "https://web.archive.org/web/20180428070843/" - "http://dvdisaster.net/en/index.html")) + (string-append datadir "/pixmaps/dvdisaster.xpm")))))))) + (home-page "https://dvdisaster.jcea.es/") (synopsis "Error correcting codes for optical media images") (description "Optical media (CD,DVD,BD) keep their data only for a finite time (typically for many years). After that time, data loss develops -- cgit 1.4.1 From 55bef80580c391677c22fb1eeed14a8bf86a223f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 7 Nov 2021 22:03:39 +0100 Subject: gnu: dvdisaster: Remove uninstallation script. * gnu/packages/cdrom.scm (dvdisaster)[arguments]: Add a new 'remove-uninstall-script phase. --- gnu/packages/cdrom.scm | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/cdrom.scm b/gnu/packages/cdrom.scm index 3a7e7b0e3b..717d59f0e9 100644 --- a/gnu/packages/cdrom.scm +++ b/gnu/packages/cdrom.scm @@ -465,7 +465,12 @@ or @command{xorrisofs} to create ISO 9660 images.") (find-files "contrib" "dvdisaster[0-9]*\\.png")) (mkdir-p (string-append datadir "/pixmaps")) (copy-file "contrib/dvdisaster48.xpm" - (string-append datadir "/pixmaps/dvdisaster.xpm")))))))) + (string-append datadir "/pixmaps/dvdisaster.xpm"))))) + (add-after 'install 'remove-uninstall-script + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out"))) + (delete-file + (string-append out "/bin/dvdisaster-uninstall.sh")))))))) (home-page "https://dvdisaster.jcea.es/") (synopsis "Error correcting codes for optical media images") (description "Optical media (CD,DVD,BD) keep their data only for a -- cgit 1.4.1 From b331ee62f532baf36e4bb50b376279d51a34e534 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 7 Nov 2021 22:10:12 +0100 Subject: gnu: lilv: Update to 0.24.12. * gnu/packages/audio.scm (lilv): Update to 0.24.12. [arguments]: Don't explicitly return #t from phases. --- gnu/packages/audio.scm | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 7cfbfc731d..3229fb5605 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -2612,14 +2612,14 @@ frequencies. This data is then formatted to MIDI and written to disk.") (define-public lilv (package (name "lilv") - (version "0.24.10") + (version "0.24.12") (source (origin (method url-fetch) (uri (string-append "https://download.drobilla.net/lilv-" version ".tar.bz2")) (sha256 (base32 - "1565zy0yz46cf2f25pi46msdnzkj6bbhml9gfigdpjnsdlyskfyi")))) + "0qchfsyrsrp2pdpd59025kllycr04ddpzd03ha1iz70ci687g8r6")))) (build-system waf-build-system) (arguments `(#:tests? #f ; no check target @@ -2629,15 +2629,13 @@ frequencies. This data is then formatted to MIDI and written to disk.") (lambda* (#:key outputs #:allow-other-keys) (setenv "LDFLAGS" (string-append "-Wl,-rpath=" - (assoc-ref outputs "out") "/lib")) - #t)) + (assoc-ref outputs "out") "/lib")))) (add-after 'unpack 'full-store-path-to-shared-library (lambda* (#:key outputs #:allow-other-keys) (with-directory-excursion "bindings/python" (substitute* "lilv.py" (("liblilv-0.so") (string-append (assoc-ref outputs "out") - "/lib/liblilv-0.so")))) - #t))))) + "/lib/liblilv-0.so"))))))))) ;; Required by lilv-0.pc. (propagated-inputs `(("lv2" ,lv2) -- cgit 1.4.1 From c569c735c267797a55f84574f7ae1e81832c3906 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 7 Nov 2021 22:10:26 +0100 Subject: gnu: jalv: Update to 1.6.6. * gnu/packages/audio.scm (jalv): Update to 1.6.6. --- gnu/packages/audio.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 3229fb5605..5be00a31cf 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -2207,14 +2207,14 @@ synchronous execution of all clients, and low latency operation.") (define-public jalv (package (name "jalv") - (version "1.6.4") + (version "1.6.6") (source (origin (method url-fetch) (uri (string-append "https://download.drobilla.net/jalv-" version ".tar.bz2")) (sha256 (base32 - "1wwfn7yzbs37s2rdlfjgks63svd5g14yyzd2gdl7h0z12qncwsy2")))) + "05lycfq0f06zjp5xqvzjz9hx9kmqx72yng1lghh76hv63dw43lcj")))) (build-system waf-build-system) (arguments `(#:tests? #f ; no check target -- cgit 1.4.1 From 6a36f4e4fcfa589463ac2f009bc83de32a76c2c4 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 7 Nov 2021 22:10:51 +0100 Subject: gnu: lv2: Update to 1.18.2. * gnu/packages/audio.scm (lv2): Update to 1.18.2. --- gnu/packages/audio.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 5be00a31cf..f41f23f35e 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -2656,14 +2656,14 @@ significantly faster and have minimal dependencies.") (define-public lv2 (package (name "lv2") - (version "1.18.0") + (version "1.18.2") (source (origin (method url-fetch) (uri (string-append "https://lv2plug.in/spec/lv2-" version ".tar.bz2")) (sha256 (base32 - "0gs7401xz23q9vajqr31aa2db8dvssgyh5zrvr4ipa6wig7yb8wh")))) + "0pp0n9x1rg8d4fw853z9cvfifjdi4bl85yjxxddqa1acfjy1z2af")))) (build-system waf-build-system) (arguments `(#:tests? #f ; no check target -- cgit 1.4.1 From 031906be767dd4e21261b862915d77095177ccd2 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 7 Nov 2021 22:49:08 +0100 Subject: gnu: xfstests: Update to 1.1.0-1.bae1d15. * gnu/packages/file-systems.scm (xfstests): Update to 1.1.0-1.bae1d15. --- gnu/packages/file-systems.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/file-systems.scm b/gnu/packages/file-systems.scm index 68488301b3..e897bdd2d7 100644 --- a/gnu/packages/file-systems.scm +++ b/gnu/packages/file-systems.scm @@ -1028,8 +1028,8 @@ APFS.") (define-public xfstests ;; The last release (1.1.0) is from 2011. - (let ((revision "0") - (commit "1c18b9ec2fcc94bd05ecdd136aa51c97bf3fa70d")) + (let ((revision "1") + (commit "bae1d15f6421cbe99b3e2e134c39d50248e7c261")) (package (name "xfstests") (version (git-version "1.1.0" revision commit)) @@ -1041,7 +1041,7 @@ APFS.") (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "0rrv0rs9nhaza0jk5k0bj27w4lcd1s4a1ls8nr679qi02bgx630x")))) + (base32 "01y7dx5sx1xg3dycqlp2b6azclz3xcnx7vdy2rr6zmf210501xd9")))) (build-system gnu-build-system) (arguments `(#:phases -- cgit 1.4.1 From 90cd653abee6288004ebc1e3d38b14e094fb5364 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 7 Nov 2021 22:50:55 +0100 Subject: gnu: ansible-core: Update to 2.11.6. * gnu/packages/admin.scm (ansible-core): Update to 2.11.6. --- gnu/packages/admin.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index b17a331ed4..7e560834b4 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -2507,14 +2507,13 @@ of supported upstream metrics systems simultaneously.") (define-public ansible-core (package (name "ansible-core") - (version "2.11.4") + (version "2.11.6") (source (origin (method url-fetch) (uri (pypi-uri "ansible-core" version)) (sha256 - (base32 - "0jgahcv2pyc5ky0wir55a1h9q9d6rgqj60rqmvlpbj76vz1agsi2")))) + (base32 "0fih7nxszni8imi5sywsifd976v77ydhip43pzg7dd65qy1h5mck")))) (build-system python-build-system) (arguments `(#:modules ((guix build python-build-system) -- cgit 1.4.1 From dab2ac2ed53810427bb6a053137091d8d9ab3e56 Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Sun, 7 Nov 2021 22:25:34 +0100 Subject: gnu: 0ad: Update to 0.0.25b-alpha. * gnu/packages/games.scm (0ad-data): Update to 0.0.25b-alpha. Unpack .zip files without need for a snippet. (0ad): Update to 0.0.25b-alpha. [arguments]<#:phases>: Properly unbundle cxxtest. Respect #:tests?. Install Freedesktop mimeinfo. Install icon to hicolor theme instead of share/pixmaps, which I don't think is used. <#:tests> Disable tests for now since they don't run. Signed-off-by: Nicolas Goaziou --- gnu/packages/games.scm | 96 +++++++++++++++++++++++++++----------------------- 1 file changed, 51 insertions(+), 45 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 1e5f0a1e9a..f33ee8795b 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -65,6 +65,8 @@ ;;; Copyright © 2021 Solene Rapenne ;;; Copyright © 2021 Noisytoot ;;; Copyright © 2021 Petr Hodina +;;; Copyright © 2021 Brendan Tildesley +;;; Copyright © 2021 Christopher Baines ;;; ;;; This file is part of GNU Guix. ;;; @@ -151,6 +153,7 @@ #:use-module (gnu packages less) #:use-module (gnu packages libcanberra) #:use-module (gnu packages libedit) + #:use-module (gnu packages libidn) #:use-module (gnu packages libunwind) #:use-module (gnu packages linux) #:use-module (gnu packages llvm) @@ -171,6 +174,7 @@ #:use-module (gnu packages perl-check) #:use-module (gnu packages perl-compression) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages pretty-print) #:use-module (gnu packages protobuf) #:use-module (gnu packages pulseaudio) #:use-module (gnu packages python) @@ -6667,7 +6671,7 @@ fight against their plot and save his fellow rabbits from slavery.") (define-public 0ad-data (package (name "0ad-data") - (version "0.0.23b-alpha") + (version "0.0.25b-alpha") (source (origin (method url-fetch) @@ -6675,21 +6679,10 @@ fight against their plot and save his fellow rabbits from slavery.") version "-unix-data.tar.xz")) (file-name (string-append name "-" version ".tar.xz")) (sha256 - (base32 - "04x7729hk6zw1xj3n4s4lvaviijsnbjf5rhzvjxlr5fygvg4l6z1")) - (modules '((guix build utils))) - (snippet - #~(begin - (for-each (lambda (name) - (let* ((dir (string-append "binaries/data/mods/" name)) - (file (string-append dir "/" name ".zip")) - (unzip #$(file-append unzip "/bin/unzip"))) - (invoke unzip "-d" dir file) - (delete-file file))) - '("mod" "public")) - #t)))) + (base32 "1c9zrddmjxvvacismld6fbwbw9vrdbq6g6d3424p8w5p6xg5wlwy")))) (build-system trivial-build-system) (native-inputs `(("tar" ,tar) + ("unzip" ,unzip) ("xz" ,xz))) (arguments `(#:modules ((guix build utils)) @@ -6699,10 +6692,18 @@ fight against their plot and save his fellow rabbits from slavery.") (let ((out (assoc-ref %outputs "out")) (source (assoc-ref %build-inputs "source")) (tar (string-append (assoc-ref %build-inputs "tar") "/bin/tar")) + (unzip (string-append (assoc-ref %build-inputs "unzip") + "/bin/unzip")) (xz-path (string-append (assoc-ref %build-inputs "xz") "/bin"))) (setenv "PATH" xz-path) (mkdir out) - (invoke tar "xvf" source "-C" out "--strip=3"))))) + (invoke tar "xvf" source "-C" out "--strip=3") + (for-each (lambda (name) + (let* ((dir (string-append out "/mods/" name)) + (file (string-append dir "/" name ".zip"))) + (invoke unzip "-o" "-d" dir file) + (delete-file file))) + '("mod" "public")))))) (synopsis "Data files for 0ad") (description "0ad-data provides the data files required by the game 0ad.") (home-page "https://play0ad.com") @@ -6720,7 +6721,7 @@ fight against their plot and save his fellow rabbits from slavery.") (define-public 0ad (package (name "0ad") - (version "0.0.23b-alpha") + (version "0.0.25b-alpha") (source (origin (method url-fetch) @@ -6728,23 +6729,24 @@ fight against their plot and save his fellow rabbits from slavery.") version "-unix-build.tar.xz")) (file-name (string-append name "-" version ".tar.xz")) (sha256 - (base32 - "0draa53xg69i5qhqym85658m45xhwkbiimaldj4sr3703rjgggq1")))) - ;; A snippet here would cause a build failure because of timestamps - ;; reset. See https://bugs.gnu.org/26734. + (base32 "1p9fa8f7sjb9c5wl3mawzyfqvgr614kdkhrj2k4db9vkyisws3fp")))) + ;; A snippet here would cause a build failure because of timestamps + ;; reset. See https://bugs.gnu.org/26734. (inputs `(("0ad-data" ,0ad-data) ("curl" ,curl) ("enet" ,enet) + ("fmt" ,fmt) ("gloox" ,gloox) - ("icu4c" ,icu4c) + ("icu4c" ,icu4c-68) + ("libidn" ,libidn) ("libpng" ,libpng) ("libsodium" ,libsodium) ("libvorbis" ,libvorbis) ("libxcursor" ,libxcursor) ("libxml2" ,libxml2) ("miniupnpc" ,miniupnpc) - ("mozjs-38" ,mozjs-38) + ("mozjs" ,mozjs-78) ("openal" ,openal) ("sdl2" ,sdl2) ("wxwidgets" ,wxwidgets) @@ -6752,29 +6754,27 @@ fight against their plot and save his fellow rabbits from slavery.") (native-inputs `(("boost" ,boost) ("cmake" ,cmake-minimal) + ("cxxtest" ,cxxtest) ("mesa" ,mesa) ("pkg-config" ,pkg-config) ("python-2" ,python-2))) (build-system gnu-build-system) (arguments `(#:make-flags '("config=release" "verbose=1" "-C" "build/workspaces/gcc") + #:tests? #f ;tests fail currently #:phases (modify-phases %standard-phases (add-after 'unpack 'delete-bundles - (lambda _ + (lambda* (#:key inputs #:allow-other-keys) (delete-file-recursively "libraries/source/spidermonkey") - #t)) - (add-after 'unpack 'fix-x11-includes - (lambda _ - (substitute* "source/lib/sysdep/os/unix/x/x.cpp" - (("") "")) - (substitute* "source/lib/sysdep/os/unix/x/x.cpp" - (("") "")) - (substitute* "source/lib/sysdep/os/unix/x/x.cpp" - (("") "")) - #t)) + (delete-file-recursively "libraries/source/cxxtest-4.4") + (substitute* "build/premake/premake5.lua" + (("rootdir\\.\\.\"\\/libraries\\/source\\/cxxtest-4.4\\/bin\\/cxxtestgen\"") + (string-append "\"" (assoc-ref inputs "cxxtest") + "/bin/cxxtestgen" + "\""))))) (replace 'configure - (lambda* (#:key inputs outputs #:allow-other-keys) + (lambda* (#:key inputs outputs tests? #:allow-other-keys) (let* ((jobs (number->string (parallel-job-count))) (out (assoc-ref outputs "out")) (lib (string-append out "/lib")) @@ -6782,11 +6782,13 @@ fight against their plot and save his fellow rabbits from slavery.") (setenv "JOBS" (string-append "-j" jobs)) (setenv "CC" "gcc") (with-directory-excursion "build/workspaces" - (invoke "./update-workspaces.sh" - (string-append "--libdir=" lib) - (string-append "--datadir=" data) - ;; TODO: "--with-system-nvtt" - "--with-system-mozjs38"))))) + (apply invoke + `("./update-workspaces.sh" + ,(string-append "--libdir=" lib) + ,(string-append "--datadir=" data) + ;; TODO: "--with-system-nvtt" + "--with-system-mozjs" + ,@(if tests? '() '("--without-tests")))))))) (delete 'check) (replace 'install (lambda* (#:key inputs outputs #:allow-other-keys) @@ -6796,7 +6798,9 @@ fight against their plot and save his fellow rabbits from slavery.") (lib (string-append out "/lib")) (data (string-append out "/share/0ad")) (applications (string-append out "/share/applications")) - (pixmaps (string-append out "/share/pixmaps")) + (hicolor (string-append out "/share/icons/hicolor/128x128/apps")) + (metainfo (string-append out "/share/metainfo")) + (mime (string-append out "/share/mime/application")) (0ad-data (assoc-ref inputs "0ad-data"))) ;; data (copy-recursively "data" data) @@ -6815,12 +6819,14 @@ fight against their plot and save his fellow rabbits from slavery.") ;; resources (with-directory-excursion "../build/resources" (install-file "0ad.desktop" applications) - (install-file "0ad.png" pixmaps)) - #t))) + (install-file "0ad.png" hicolor) + (install-file "0ad.appdata.xml" metainfo) + (install-file "pyrogenesis.xml" mime))))) (add-after 'install 'check - (lambda _ - (with-directory-excursion "system" - (invoke "./test"))))))) + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (with-directory-excursion "system" + (invoke "./test")))))))) (home-page "https://play0ad.com") (synopsis "3D real-time strategy game of ancient warfare") (description "0 A.D. is a real-time strategy (RTS) game of ancient -- cgit 1.4.1 From 5eb5c0789f34e87ee417a53ddfcfa3b6521bb337 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Sun, 7 Nov 2021 18:42:11 +0100 Subject: file-systems: Validate the 'flags' field. Fixes . Reported by Jonathan Brielmaier . * gnu/system/file-systems.scm (invalid-file-system-flags) (%validate-file-system-flags): New procedures. (validate-file-system-flags): New macro. ()[flags]: Add 'sanitize' property. --- gnu/system/file-systems.scm | 47 ++++++++++++++++++++++++++++++++++++++++++--- 1 file changed, 44 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/system/file-systems.scm b/gnu/system/file-systems.scm index e69cfd06e6..c6c1b96d16 100644 --- a/gnu/system/file-systems.scm +++ b/gnu/system/file-systems.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès +;;; Copyright © 2013-2021 Ludovic Courtès ;;; Copyright © 2020 Google LLC ;;; Copyright © 2020 Jakub Kądziołka ;;; Copyright © 2020, 2021 Maxim Cournoyer @@ -30,7 +30,8 @@ #:use-module (srfi srfi-35) #:use-module (srfi srfi-9 gnu) #:use-module (guix records) - #:use-module ((guix diagnostics) #:select (&fix-hint)) + #:use-module ((guix diagnostics) + #:select (source-properties->location leave &fix-hint)) #:use-module (guix i18n) #:use-module (gnu system uuid) #:re-export (uuid ;backward compatibility @@ -107,6 +108,45 @@ ;;; ;;; Code: +(eval-when (expand load eval) + (define invalid-file-system-flags + ;; Note: Keep in sync with 'mount-flags->bit-mask'. + (let ((known-flags '(read-only + bind-mount no-suid no-dev no-exec + no-atime strict-atime lazy-time))) + (lambda (flags) + "Return the subset of FLAGS that is invalid." + (remove (cut memq <> known-flags) flags)))) + + (define (%validate-file-system-flags flags location) + "Raise an error if FLAGS contains invalid mount flags; otherwise return +FLAGS." + (match (invalid-file-system-flags flags) + (() flags) + (invalid + (leave (source-properties->location location) + (N_ "invalid file system mount flag:~{ ~s~}~%" + "invalid file system mount flags:~{ ~s~}~%" + (length invalid)) + invalid))))) + +(define-syntax validate-file-system-flags + (lambda (s) + "Validate the given file system mount flags, raising an error if invalid +flags are found." + (syntax-case s (quote) + ((_ (quote (symbols ...))) ;validate at expansion time + (begin + (%validate-file-system-flags (syntax->datum #'(symbols ...)) + (syntax-source s)) + #'(quote (symbols ...)))) + ((_ flags) + #`(%validate-file-system-flags flags + '#,(datum->syntax s (syntax-source s)))) + (id + (identifier? #'id) + #'%validate-file-system-flags)))) + ;; File system declaration. (define-record-type* %file-system make-file-system @@ -115,7 +155,8 @@ (mount-point file-system-mount-point) ; string (type file-system-type) ; string (flags file-system-flags ; list of symbols - (default '())) + (default '()) + (sanitize validate-file-system-flags)) (options file-system-options ; string or #f (default #f)) (mount? file-system-mount? ; Boolean -- cgit 1.4.1 From 4b96998292442ec03024481c911d88f86c7c36b5 Mon Sep 17 00:00:00 2001 From: Xinglu Chen Date: Sun, 7 Nov 2021 12:36:19 +0100 Subject: home: services: bash: Add ‘aliases’ field. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * doc/guix.texi (Shells Home Services): Document it. * gnu/home/services/shells.scm (bash-serialize-aliases): New procedure. (home-bash-configuration, home-bash-extension): Add ‘aliases’ field. (home-bash-extensions): Adjust accordingly. * guix/scripts/home/import.scm (generate-bash-configuration+modules): Populate the ‘alias’ field. Signed-off-by: Ludovic Courtès --- doc/guix.texi | 14 ++++++++ gnu/home/services/shells.scm | 83 ++++++++++++++++++++++++++++++++------------ guix/scripts/home/import.scm | 24 +++++++++++++ 3 files changed, 98 insertions(+), 23 deletions(-) (limited to 'gnu') diff --git a/doc/guix.texi b/doc/guix.texi index b35fb35770..6d6dfd5177 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -36173,6 +36173,20 @@ Add sane defaults like reading @file{/etc/bashrc}, coloring output for @item @code{environment-variables} (default: @code{()}) (type: alist) Association list of environment variables to set for the Bash session. +@item @code{aliases} (default: @code{()}) (type: alist) +Association list of aliases to set for the Bash session. The alias will +automatically be quoted, so something line this: + +@lisp +'((\"ls\" . \"ls -alF\")) +@end lisp + +turns into + +@example +alias ls=\"ls -alF\" +@end example + @item @code{bash-profile} (default: @code{()}) (type: text-config) List of file-like objects, which will be added to @file{.bash_profile}. Used for executing user's commands at start of login shell (In most diff --git a/gnu/home/services/shells.scm b/gnu/home/services/shells.scm index e2730967b2..f24e47f762 100644 --- a/gnu/home/services/shells.scm +++ b/gnu/home/services/shells.scm @@ -305,6 +305,18 @@ source ~/.profile ;;; Bash. ;;; +(define (bash-serialize-aliases field-name val) + #~(string-append + #$@(map + (match-lambda + ((key . #f) + "") + ((key . #t) + #~(string-append "alias " #$key "\n")) + ((key . value) + #~(string-append "alias " #$key "=\"" #$value "\"\n"))) + val))) + (define-configuration home-bash-configuration (package (package bash) @@ -317,6 +329,21 @@ for @code{ls} provided by guix to @file{.bashrc}.") (alist '()) "Association list of environment variables to set for the Bash session." serialize-posix-env-vars) + (aliases + (alist '()) + "Association list of aliases to set for the Bash session. The alias will +automatically be quoted, so something line this: + +@lisp +'((\"ls\" . \"ls -alF\")) +@end lisp + +turns into + +@example +alias ls=\"ls -alF\" +@end example" + bash-serialize-aliases) (bash-profile (text-config '()) "List of file-like objects, which will be added to @file{.bash_profile}. @@ -387,10 +414,10 @@ alias grep='grep --color=auto'\n") (if (or extra-content (not (null? ((configuration-field-getter field-obj) config)))) `(,(object->snake-case-string file-name) - ,(mixed-text-file + ,(apply mixed-text-file (object->snake-case-string file-name) - (if extra-content extra-content "") - (serialize-field field))) + (cons (serialize-field field) + (if extra-content extra-content '())))) '()))) (filter @@ -413,8 +440,8 @@ if [ -f ~/.bashrc ]; then source ~/.bashrc; fi ,@(list (file-if-not-empty 'bashrc (if (home-bash-configuration-guix-defaults? config) - guix-bashrc - #f)) + (list (serialize-field 'aliases) guix-bashrc) + (list (serialize-field 'alises)))) (file-if-not-empty 'bash-logout))))) (define (add-bash-packages config) @@ -424,6 +451,9 @@ if [ -f ~/.bashrc ]; then source ~/.bashrc; fi (environment-variables (alist '()) "Association list of environment variables to set.") + (aliases + (alist '()) + "Association list of aliases to set.") (bash-profile (text-config '()) "List of file-like objects.") @@ -435,24 +465,31 @@ if [ -f ~/.bashrc ]; then source ~/.bashrc; fi "List of file-like objects.")) (define (home-bash-extensions original-config extension-configs) - (home-bash-configuration - (inherit original-config) - (environment-variables - (append (home-bash-configuration-environment-variables original-config) - (append-map - home-bash-extension-environment-variables extension-configs))) - (bash-profile - (append (home-bash-configuration-bash-profile original-config) - (append-map - home-bash-extension-bash-profile extension-configs))) - (bashrc - (append (home-bash-configuration-bashrc original-config) - (append-map - home-bash-extension-bashrc extension-configs))) - (bash-logout - (append (home-bash-configuration-bash-logout original-config) - (append-map - home-bash-extension-bash-logout extension-configs))))) + (match original-config + (($ _ _ _ environment-variables aliases + bash-profile bashrc bash-logout) + (home-bash-configuration + (inherit original-config) + (environment-variables + (append environment-variables + (append-map + home-bash-extension-environment-variables extension-configs))) + (aliases + (append aliases + (append-map + home-bash-extension-aliases extension-configs))) + (bash-profile + (append bash-profile + (append-map + home-bash-extension-bash-profile extension-configs))) + (bashrc + (append bashrc + (append-map + home-bash-extension-bashrc extension-configs))) + (bash-logout + (append bash-logout + (append-map + home-bash-extension-bash-logout extension-configs))))))) (define home-bash-service-type (service-type (name 'home-bash) diff --git a/guix/scripts/home/import.scm b/guix/scripts/home/import.scm index 7a7712dd96..fbf89069a7 100644 --- a/guix/scripts/home/import.scm +++ b/guix/scripts/home/import.scm @@ -27,6 +27,9 @@ #:use-module (gnu packages) #:use-module (ice-9 match) #:use-module (ice-9 pretty-print) + #:use-module (ice-9 rdelim) + #:use-module (ice-9 regex) + #:use-module (ice-9 popen) #:use-module (srfi srfi-1) #:use-module (srfi srfi-26) #:export (import-manifest @@ -56,11 +59,32 @@ FILE-NAME with \"-\", and return the basename of it." (define (destination-append path) (string-append destination-directory "/" path)) + (define (bash-alias->pair line) + (if (string-prefix? "alias" line) + (let ((matched (string-match "alias (.+)=\"?'?([^\"']+)\"?'?" line))) + `(,(match:substring matched 1) . ,(match:substring matched 2))) + '())) + + (define (parse-aliases input) + (let loop ((line (read-line input)) + (result '())) + (if (eof-object? line) + (reverse result) + (loop (read-line input) + (cons (bash-alias->pair line) result))))) + (let ((rc (destination-append ".bashrc")) (profile (destination-append ".bash_profile")) (logout (destination-append ".bash_logout"))) `((service home-bash-service-type (home-bash-configuration + ,@(if (file-exists? rc) + `((aliases + ',(let* ((port (open-pipe* OPEN_READ "bash" "-i" "-c" "alias")) + (alist (parse-aliases port))) + (close-port port) + (filter (negate null?) alist)))) + '()) ,@(if (file-exists? rc) `((bashrc (list (local-file ,rc -- cgit 1.4.1 From 2f665d4309053d5a9fe25bc93ee78d55dbc30cb7 Mon Sep 17 00:00:00 2001 From: Xinglu Chen Date: Sun, 7 Nov 2021 12:36:29 +0100 Subject: doc: Improve documentation of the Bash home service MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * doc/guix.texi (Shells Home Services): Document ‘home-bash-extension’ configuration record. * gnu/home/services/shells.scm (generate-home-bash-documentation): Extract docstrings from ‘home-bash-extension’. (home-bash-configuration): Expound on docstrings. (home-bash-extension): Likewise. Fixes: Signed-off-by: Ludovic Courtès --- doc/guix.texi | 50 +++++++++++++++++++++++++++++++++++++++----- gnu/home/services/shells.scm | 45 ++++++++++++++++++++++++++------------- 2 files changed, 76 insertions(+), 19 deletions(-) (limited to 'gnu') diff --git a/doc/guix.texi b/doc/guix.texi index 6d6dfd5177..76290d593e 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -36159,6 +36159,7 @@ Extend home-shell-profile service only if you really know what you do. @subsubheading Bash Home Service +@anchor{home-bash-configuration} @deftp {Data Type} home-bash-configuration Available @code{home-bash-configuration} fields are: @@ -36167,15 +36168,20 @@ Available @code{home-bash-configuration} fields are: The Bash package to use. @item @code{guix-defaults?} (default: @code{#t}) (type: boolean) -Add sane defaults like reading @file{/etc/bashrc}, coloring output for -@code{ls} provided by guix to @file{.bashrc}. +Add sane defaults like reading @file{/etc/bashrc} and coloring the output of +@command{ls} to the end of the @file{.bashrc} file. @item @code{environment-variables} (default: @code{()}) (type: alist) -Association list of environment variables to set for the Bash session. +Association list of environment variables to set for the Bash session. The +rules for the @code{home-environment-variables-service-type} apply +here (@pxref{Essential Home Services}). The contents of this field will be +added after the contents of the @code{bash-profile} field. @item @code{aliases} (default: @code{()}) (type: alist) -Association list of aliases to set for the Bash session. The alias will -automatically be quoted, so something line this: +Association list of aliases to set for the Bash session. The aliases +will be defined after the contents of the @code{bashrc} field has been +put in the @file{.bashrc} file. The alias will automatically be quoted, +so something line this: @lisp '((\"ls\" . \"ls -alF\")) @@ -36206,7 +36212,41 @@ be read in some cases (if the shell terminates by exec'ing another process for example). @end table +@end deftp + +You can extend the Bash service by using the @code{home-bash-extension} +configuration record, whose fields most mirror that of +@code{home-bash-configuration} (@pxref{home-bash-configuration}). The +contents of the extensions will be added to the end of the corresponding +Bash configuration files (@pxref{Bash Startup Files,,, bash, The GNU +Bash Reference Manual}. + +@deftp {Data Type} home-bash-extension +Available @code{home-bash-extension} fields are: + +@table @asis +@item @code{environment-variables} (default: @code{()}) (type: alist) +Additional environment variables to set. These will be combined with the +environment variables from other extensions and the base service to form one +coherent block of environment variables. + +@item @code{aliases} (default: @code{()}) (type: alist) +Additional aliases to set. These will be combined with the aliases from +other extensions and the base service. +@item @code{bash-profile} (default: @code{()}) (type: text-config) +Additional text blocks to add to @file{.bash_profile}, which will be combined +with text blocks from other extensions and the base service. + +@item @code{bashrc} (default: @code{()}) (type: text-config) +Additional text blocks to add to @file{.bashrc}, which will be combined +with text blocks from other extensions and the base service. + +@item @code{bash-logout} (default: @code{()}) (type: text-config) +Additional text blocks to add to @file{.bash_logout}, which will be combined +with text blocks from other extensions and the base service. + +@end table @end deftp @subsubheading Zsh Home Service diff --git a/gnu/home/services/shells.scm b/gnu/home/services/shells.scm index f24e47f762..81d07da86c 100644 --- a/gnu/home/services/shells.scm +++ b/gnu/home/services/shells.scm @@ -323,16 +323,21 @@ source ~/.profile "The Bash package to use.") (guix-defaults? (boolean #t) - "Add sane defaults like reading @file{/etc/bashrc}, coloring output -for @code{ls} provided by guix to @file{.bashrc}.") + "Add sane defaults like reading @file{/etc/bashrc} and coloring the output of +@command{ls} to the end of the @file{.bashrc} file.") (environment-variables (alist '()) - "Association list of environment variables to set for the Bash session." + "Association list of environment variables to set for the Bash session. The +rules for the @code{home-environment-variables-service-type} apply +here (@pxref{Essential Home Services}). The contents of this field will be +added after the contents of the @code{bash-profile} field." serialize-posix-env-vars) (aliases (alist '()) - "Association list of aliases to set for the Bash session. The alias will -automatically be quoted, so something line this: + "Association list of aliases to set for the Bash session. The aliases will be +defined after the contents of the @code{bashrc} field has been put in the +@file{.bashrc} file. The alias will automatically be quoted, so something line +this: @lisp '((\"ls\" . \"ls -alF\")) @@ -450,19 +455,25 @@ if [ -f ~/.bashrc ]; then source ~/.bashrc; fi (define-configuration/no-serialization home-bash-extension (environment-variables (alist '()) - "Association list of environment variables to set.") + "Additional environment variables to set. These will be combined with the +environment variables from other extensions and the base service to form one +coherent block of environment variables.") (aliases (alist '()) - "Association list of aliases to set.") + "Additional aliases to set. These will be combined with the aliases from +other extensions and the base service.") (bash-profile (text-config '()) - "List of file-like objects.") + "Additional text blocks to add to @file{.bash_profile}, which will be combined +with text blocks from other extensions and the base service.") (bashrc (text-config '()) - "List of file-like objects.") + "Additional text blocks to add to @file{.bashrc}, which will be combined +with text blocks from other extensions and the base service.") (bash-logout (text-config '()) - "List of file-like objects.")) + "Additional text blocks to add to @file{.bash_logout}, which will be combined +with text blocks from other extensions and the base service.")) (define (home-bash-extensions original-config extension-configs) (match original-config @@ -646,10 +657,16 @@ Install and configure Fish, the friendly interactive shell."))) 'home-shell-profile-configuration)) (define (generate-home-bash-documentation) - (generate-documentation - `((home-bash-configuration - ,home-bash-configuration-fields)) - 'home-bash-configuration)) + (string-append + (generate-documentation + `((home-bash-configuration + ,home-bash-configuration-fields)) + 'home-bash-configuration) + "\n\n" + (generate-documentation + `((home-bash-extension + ,home-bash-extension-fields)) + 'home-bash-extension))) (define (generate-home-zsh-documentation) (generate-documentation -- cgit 1.4.1 From bd41e590dd24e54797fb8b6854c244efd4d12df5 Mon Sep 17 00:00:00 2001 From: Thorsten Wilms Date: Wed, 3 Nov 2021 11:53:10 +0100 Subject: gnu: ardour: Update to 6.9. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/audio.scm (ardour): Update to 6.9. Signed-off-by: Ludovic Courtès --- gnu/packages/audio.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index f41f23f35e..5b3d9f3940 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -15,7 +15,7 @@ ;;; Copyright © 2018 Clément Lassieur ;;; Copyright © 2018 Brett Gilio ;;; Copyright © 2018, 2019 Marius Bakke -;;; Copyright © 2018 Thorsten Wilms +;;; Copyright © 2018, 2021 Thorsten Wilms ;;; Copyright © 2018 Eric Bavier ;;; Copyright © 2018 Brendan Tildesley ;;; Copyright © 2019, 2021 Pierre Langlois @@ -616,7 +616,7 @@ streams from live audio.") (define-public ardour (package (name "ardour") - (version "6.8") + (version "6.9") (source (origin (method git-fetch) (uri (git-reference @@ -634,7 +634,7 @@ namespace ARDOUR { const char* revision = \"" version "\" ; const char* date = \ #t))) (sha256 (base32 - "16x7bkzbrk0rgywq5vrkhf2z3jj08jw1bvaq9vwlf2b4h4sd7i4s")) + "0vlcbd70y0an881zv87kc3akmaiz4w7whsy3yaiiqqjww35jg1mm")) (file-name (string-append name "-" version)))) (build-system waf-build-system) (arguments -- cgit 1.4.1 From 17d0bbef88501126f13f9b60aa74d3c912c853ed Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 09:39:50 +0000 Subject: gnu: r-with-tests: Update to 4.1.2. * gnu/packages/statistics.scm (r-with-tests): Update to 4.1.2. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index bad2e774e1..038258a8bc 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -190,7 +190,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") (define r-with-tests (package (name "r-with-tests") - (version "4.1.1") + (version "4.1.2") (source (origin (method url-fetch) (uri (string-append "mirror://cran/src/base/R-" @@ -198,7 +198,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") version ".tar.gz")) (sha256 (base32 - "0r6kpnxjbvb7gdfg4m1z8zc6xd225vw81wrnf05ps9ajawk06pji")))) + "1brqmc7mmb0z94kcs4crgl6v9a6sxhm9fm3y177d81vjkxg24di0")))) (build-system gnu-build-system) (arguments `(#:disallowed-references (,tzdata-for-tests) -- cgit 1.4.1 From 108111114d5269e608f961d44955d0d4613b9c15 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 09:40:41 +0000 Subject: gnu: r-with-tests: Remove trailing #T. * gnu/packages/statistics.scm (r-with-tests)[arguments]: Remove trailing #T from build phases. --- gnu/packages/statistics.scm | 17 ++++++----------- 1 file changed, 6 insertions(+), 11 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 038258a8bc..eb6898e60d 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -215,8 +215,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") ;; This ensures that Guix can detect embedded store references; ;; see bug #28157 for details. (substitute* "src/library/base/makebasedb.R" - (("compress = TRUE") "compress = FALSE")) - #t)) + (("compress = TRUE") "compress = FALSE")))) (add-before 'configure 'patch-coreutils-paths (lambda* (#:key inputs #:allow-other-keys) (let* ((coreutils (assoc-ref inputs "coreutils")) @@ -225,8 +224,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") (substitute* "src/scripts/R.sh.in" (("uname") uname-bin)) (substitute* "src/unix/sys-std.c" - (("rm -Rf ") (string-append rm-bin " -Rf ")))) - #t)) + (("rm -Rf ") (string-append rm-bin " -Rf ")))))) (add-after 'unpack 'build-reproducibly (lambda _ ;; The documentation contains time stamps to demonstrate @@ -285,17 +283,15 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\ ;; that is suspected to be the culprit. (substitute* "src/library/methods/DESCRIPTION.in" (("\\(2008\\)\n") "(2008) ") - ((" ``Software") "``Software")) - #t)) + ((" ``Software") "``Software")))) (add-before 'build 'set-locales (lambda _ (setlocale LC_ALL "C") - (setenv "LC_ALL" "C") - #t)) + (setenv "LC_ALL" "C"))) (add-before 'configure 'set-default-pager ;; Set default pager to "cat", because otherwise it is "false", ;; making "help()" print nothing at all. - (lambda _ (setenv "PAGER" "cat") #t)) + (lambda _ (setenv "PAGER" "cat"))) (add-before 'check 'set-timezone ;; Some tests require the timezone to be set. However, the ;; timezone may not just be "UTC", or else a brittle regression @@ -304,8 +300,7 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\ (setenv "TZ" "UTC+1") (setenv "TZDIR" (string-append (assoc-ref inputs "tzdata") - "/share/zoneinfo")) - #t)) + "/share/zoneinfo")))) (add-after 'build 'make-info (lambda _ (invoke "make" "info"))) (add-after 'build 'install-info -- cgit 1.4.1 From 92b85194cded53ef368a7e7b8a7b876cc46482c0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 09:41:14 +0000 Subject: gnu: r-with-tests: Update patch to DESCRIPTION file. * gnu/packages/statistics.scm (r-with-tests)[arguments]: Patch line breaks and spaces in DESCRIPTION file to ensure reproducible build. --- gnu/packages/statistics.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index eb6898e60d..50e014ee8d 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -283,7 +283,9 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\ ;; that is suspected to be the culprit. (substitute* "src/library/methods/DESCRIPTION.in" (("\\(2008\\)\n") "(2008) ") - ((" ``Software") "``Software")))) + ((" ``Software") "``Software") + (("Data Analysis:.") "Data Analysis:\n") + (("Programming with R") " Programming with R")))) (add-before 'build 'set-locales (lambda _ (setlocale LC_ALL "C") -- cgit 1.4.1 From 4a92ab58f62156b3f906b4560538c7e0cf339452 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 17:38:09 +0000 Subject: gnu: Add r-msfeatures. * gnu/packages/bioconductor.scm (r-msfeatures): New variable. --- gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 914bf5ab09..2c61754cb3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13100,6 +13100,38 @@ well as misc helper functions, that are used across high-level data structure within the R for Mass Spectrometry packages.") (license license:artistic2.0))) +(define-public r-msfeatures + (package + (name "r-msfeatures") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MsFeatures" version)) + (sha256 + (base32 "020ifrijlzdd3qk4bhd9z4knj5d87ildrkl3wcmxvwkvs9rbh8rq")))) + (properties `((upstream-name . "MsFeatures"))) + (build-system r-build-system) + (propagated-inputs + `(("r-mscoreutils" ,r-mscoreutils) + ("r-protgenerics" ,r-protgenerics) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/RforMassSpectrometry/MsFeatures") + (synopsis "Functionality for mass spectrometry features") + (description + "The MsFeature package defines functionality for Mass Spectrometry +features. This includes functions to group (LC-MS) features based on some of +their properties, such as retention time (coeluting features), or correlation +of signals across samples. This packge hence allows to group features, and +its results can be used as an input for the @code{QFeatures} package which +allows to aggregate abundance levels of features within each group. This +package defines concepts and functions for base and common data types, +implementations for more specific data types are expected to be implemented in +the respective packages (such as e.g. @code{xcms}).") + (license license:artistic2.0))) + (define-public r-biocio (package (name "r-biocio") -- cgit 1.4.1 From d1c79f5a2c0681d762994abee8647c86bf2549c3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 17:38:56 +0000 Subject: gnu: r-biocparallel: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.28.0. [arguments]: Adjust build phase to patch renamed file. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2c61754cb3..eb93407131 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2272,13 +2272,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.26.2") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "1y459cygq21f3igsdlxz1zlyad8qbl2qlr5h2d2dpnvblykvf48i")))) + "0jqgbpjppwinzw100qhc42kc95znq6xanl26bi8m9cq7yggbpra6")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -2306,7 +2306,7 @@ powerful online queries from gene annotation to database mining.") (("\\today") "later")) ;; Initialize the random number generator seed when building. - (substitute* "R/internal_rng_stream.R" + (substitute* "R/rng.R" (("\"L'Ecuyer-CMRG\"\\)" m) (string-append m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n")))))))) -- cgit 1.4.1 From fc0fa7a4312df2a5172902e1b840a317dbb83518 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:03:50 +0000 Subject: gnu: r-aneufinder: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-aneufinder): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index eb93407131..1aa9a30ee5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1055,13 +1055,13 @@ All datasets are restricted to protein coding genes.") (define-public r-aneufinder (package (name "r-aneufinder") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AneuFinder" version)) (sha256 (base32 - "0m6wphlriq7y21ih1p2kzml5jzcic79jc52kkk59dkjj8j88yllk")))) + "0xn8952fkchhx7m8dam6gjy86j551xp1cs67510s1qrmfgzpkjp0")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) -- cgit 1.4.1 From 6ed26516bf16d6f4125caeebb103840cadb971ed Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:03:56 +0000 Subject: gnu: r-biocversion: Update to 3.14.0. * gnu/packages/bioconductor.scm (r-biocversion): Update to 3.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1aa9a30ee5..720ad3f2cd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1401,14 +1401,14 @@ across the entire multi-'omics experiment.") (define-public r-biocversion (package (name "r-biocversion") - (version "3.13.1") + (version "3.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocVersion" version)) (sha256 (base32 - "0rsw8g4g1pcjw1zbx8x17yd3drhxqk4sx3cy3ddzy5731hl6mbfi")))) + "0qwzkh2alw7xhjprh719la0lg1q38pmjbipy3s2fy79m4xy8y8ik")))) (properties `((upstream-name . "BiocVersion"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BiocVersion/") -- cgit 1.4.1 From 3622390699032a5c1b4da82b53003686c4cba4b1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:03:56 +0000 Subject: gnu: r-biocgenerics: Update to 0.40.0. * gnu/packages/bioconductor.scm (r-biocgenerics): Update to 0.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 720ad3f2cd..7caf3c379b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1421,13 +1421,13 @@ of Bioconductor.") (define-public r-biocgenerics (package (name "r-biocgenerics") - (version "0.38.0") + (version "0.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 - "1kv7lzmyki3hi771v01nml1v1hzz8pyhqqv0xcdzqy354mlgx4m6")))) + "0nr5x4r8f2krnfrxm7wrzgzr7nbljypi985cbwx5hxhn95zmfifh")))) (properties `((upstream-name . "BiocGenerics"))) (build-system r-build-system) -- cgit 1.4.1 From 9d51c1f423f402b6c5517c265d90dee015c7c430 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:03:56 +0000 Subject: gnu: r-coverageview: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-coverageview): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7caf3c379b..42706ef989 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1441,13 +1441,13 @@ packages.") (define-public r-coverageview (package (name "r-coverageview") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CoverageView" version)) (sha256 (base32 - "1xhirbjdw09cqm4xvysxqicvqjbahavwvs7shg4cb05gwyd2ha8g")))) + "0sb1h5qsk41c9xisq73agqh502wv6p2j1k45s32a4bkdynf696as")))) (build-system r-build-system) (propagated-inputs `(("r-s4vectors" ,r-s4vectors) -- cgit 1.4.1 From 07b14e81f9d79244938eb84a850d7634110cfd84 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:03:56 +0000 Subject: gnu: r-cummerbund: Update to 2.36.0. * gnu/packages/bioconductor.scm (r-cummerbund): Update to 2.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 42706ef989..71580a01e5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1468,13 +1468,13 @@ how the coverage distributed across the genome.") (define-public r-cummerbund (package (name "r-cummerbund") - (version "2.34.0") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cummeRbund" version)) (sha256 (base32 - "1avvmvrmldbscc7xd6a6k22xjykbzafvqf87wh5z9rx3qlzswsjx")))) + "0130hrlz2jabbshis1g11ndda8b8vlirzi7a004li3cgdghscxql")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit 1.4.1 From 628a8f8c789bfb60e6518f007dd61f896f91d154 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:03:56 +0000 Subject: gnu: r-decipher: Update to 2.22.0. * gnu/packages/bioconductor.scm (r-decipher): Update to 2.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 71580a01e5..79065e36db 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1498,13 +1498,13 @@ used visualizations.") (define-public r-decipher (package (name "r-decipher") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DECIPHER" version)) (sha256 (base32 - "0mr7glkx2d37l9nszs52m0kycpm14vxl5gdp3z7i5j7yig1sw2nk")))) + "0a9k3f70jmd17kxf1zjmdzrfjs0dmwfad2zgz6wihxh5s1shc8qm")))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) -- cgit 1.4.1 From 7cc053eaca3f569b8045bef2ff998902c76a5b2b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:03:56 +0000 Subject: gnu: r-deepsnv: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-deepsnv): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 79065e36db..a7439c6065 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1522,13 +1522,13 @@ biological sequences.") (define-public r-deepsnv (package (name "r-deepsnv") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "deepSNV" version)) (sha256 (base32 - "0zz56hf417m7bgg2g2wpbaik30pi6h2nam1n5bviqgdn4mv8n0bs")))) + "1wi6j6yb6i9fs9yszfywqz3w50mhl85dkfmr4w3phwvkf0xkn81w")))) (properties `((upstream-name . "deepSNV"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 35ccf99fff00f9f3ea9973f25ce160a2118ede9f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:03:57 +0000 Subject: gnu: r-delayedarray: Update to 0.20.0. * gnu/packages/bioconductor.scm (r-delayedarray): Update to 0.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a7439c6065..1412883228 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1558,13 +1558,13 @@ bases such as COSMIC.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.18.0") + (version "0.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "0w632262dqzcnvq9s6jvc7naz93dayx51fsv05s0zb6cjwygbqjr")))) + "1cm6zh01mvhiq7zrik7q3dmgxinyjz1nyg6rfj93kpkvcb5d4wpj")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) -- cgit 1.4.1 From b0a2fc92530bb1aff599971123f153d559c8dfc7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:03:57 +0000 Subject: gnu: r-bluster: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-bluster): Update to 1.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1412883228..1a3758a6ab 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1591,13 +1591,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-bluster (package (name "r-bluster") - (version "1.2.1") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bluster" version)) (sha256 (base32 - "128zd5vwlhmrkq0bpp1dxnkrcqfz1mjmdjlla4wqbjv7v6yyn6lg")))) + "1j24l12i3aga4qd827sj8b160yvrhlznggb4piddkmhjc0sppbjm")))) (properties `((upstream-name . "bluster"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 1acf3f1821770bc08bbcb856e2a193c3beb72a4e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:03:57 +0000 Subject: gnu: r-ideoviz: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-ideoviz): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1a3758a6ab..6645603240 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1621,13 +1621,13 @@ and evaluate clustering results.") (define-public r-ideoviz (package (name "r-ideoviz") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IdeoViz" version)) (sha256 (base32 - "17sx0v5lq2zmg098ps4ksj1h0yla3vlh6s2w1ahqsq0nvm193scm")))) + "0cclk2pcb2mvsfxhw0zq3qlnfkblb1gqxnn7xypmlf0bm6hcvl4g")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit 1.4.1 From a85e744c3d48f3f857da8609ae4825b6ababe2c3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:03:57 +0000 Subject: gnu: r-iranges: Update to 2.28.0. * gnu/packages/bioconductor.scm (r-iranges): Update to 2.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6645603240..9ff8a2936e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1645,13 +1645,13 @@ arbitrary genomic intervals along chromosomal ideogram.") (define-public r-iranges (package (name "r-iranges") - (version "2.26.0") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "0dzj8wqbjzilh2dsaj3ylx958xqrv0c688ayfq2r1z7rs75qy7kx")))) + "07zs231wbfwwc1c1165rhp711fbss40p9l8kyjjv9flzpr3hr1pg")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) -- cgit 1.4.1 From 1a4e10d555de00d4c8453dd2345b95d114d71fa4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:03:57 +0000 Subject: gnu: r-affy: Update to 1.72.0. * gnu/packages/bioconductor.scm (r-affy): Update to 1.72.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9ff8a2936e..d35650089f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1803,14 +1803,14 @@ performing parallel computations on multicore machines.") (define-public r-affy (package (name "r-affy") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affy" version)) (sha256 (base32 - "0vz5y92gqcm0qk57qlba85bk683lzdr7vkmxv109rq6i17vdkkrm")))) + "0z66pyn2020h3x22xabkmnjxb20kbgblivvk7mqjk9134wvvf15a")))) (build-system r-build-system) (propagated-inputs `(("r-affyio" ,r-affyio) -- cgit 1.4.1 From a610856e880dff1cda4b16ae9502da2353c83cc4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:03:57 +0000 Subject: gnu: r-affycomp: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-affycomp): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d35650089f..cf12d9ea93 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1831,14 +1831,14 @@ analysis.") (define-public r-affycomp (package (name "r-affycomp") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycomp" version)) (sha256 (base32 - "07my5scdh6h0y1bx1h9y5m4fa8bnmw389f83gkb7cf19w4vp36b2")))) + "0kawlfff82ikrbrfyyy38zm5wj5xdri2ii9wgwilnq50z5qc6r21")))) (properties `((upstream-name . "affycomp"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase))) -- cgit 1.4.1 From 71f58a16ae5eead1c374feb076fb41d8339689b3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:03:58 +0000 Subject: gnu: r-affycompatible: Update to 1.54.0. * gnu/packages/bioconductor.scm (r-affycompatible): Update to 1.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cf12d9ea93..1657e4efe6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1852,14 +1852,14 @@ measures for Affymetrix Oligonucleotide Arrays.") (define-public r-affycompatible (package (name "r-affycompatible") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffyCompatible" version)) (sha256 (base32 - "1xwz22wf2smsvmd0d5lfadbsgscnl3fl9msypy2mml38k048p6vj")))) + "1qlfh1gcwa6akd5dhdqh260yaw1j6dap6a15ghwf74rchi5218sg")))) (properties `((upstream-name . "AffyCompatible"))) (build-system r-build-system) -- cgit 1.4.1 From 21b5db3f1e67066a61706ee77f04c7f01583c2e2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:03:58 +0000 Subject: gnu: r-affycontam: Update to 1.52.0. * gnu/packages/bioconductor.scm (r-affycontam): Update to 1.52.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1657e4efe6..09312863d1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1880,14 +1880,14 @@ Command Console} (AGCC)-compatible sample annotation files.") (define-public r-affycontam (package (name "r-affycontam") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyContam" version)) (sha256 (base32 - "0242ga68wrdk1kcmxfdbq73a0d3zhrzdlzkzphfg3q0zjbvg49jj")))) + "1vw3nxg9jvlw0zg9h70w2ww8l42qpyvgf12hsla9hyyfhj3m6i9f")))) (properties `((upstream-name . "affyContam"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 5ab6e9e100e9ae06e8a34c324a99c6b1944bf72a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:03:58 +0000 Subject: gnu: r-affycoretools: Update to 1.66.0. * gnu/packages/bioconductor.scm (r-affycoretools): Update to 1.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 09312863d1..bb837d4d99 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1905,14 +1905,14 @@ problems in CEL-level data to help evaluate performance of quality metrics.") (define-public r-affycoretools (package (name "r-affycoretools") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycoretools" version)) (sha256 (base32 - "1dx861spr3kn1dxwhf43s5l1r7bmrq0h6538l3q64iiwzzc6krdh")))) + "1ccyaj129ii9f47r41qsy34y6ck4wna55j8vz3v3hbldddn93f40")))) (properties `((upstream-name . "affycoretools"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 5de927226cf20d54aeb761932c09b0025a1d7177 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:03:58 +0000 Subject: gnu: r-affyio: Update to 1.64.0. * gnu/packages/bioconductor.scm (r-affyio): Update to 1.64.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bb837d4d99..076bba683c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1947,14 +1947,14 @@ to streamline the more common analyses that a Biostatistician might see.") (define-public r-affyio (package (name "r-affyio") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyio" version)) (sha256 (base32 - "07kibqsm888g06qqqa4648ph877kriy74kprbri8nyx83y8aspjr")))) + "02lqdq8hcldkf9qbyhhllkm3smpqc51sn2d9gbkm74r96fx37lvm")))) (build-system r-build-system) (propagated-inputs `(("r-zlibbioc" ,r-zlibbioc))) -- cgit 1.4.1 From 5b63db8f83a53c1e611671c8a2c73ac771b17498 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:03:58 +0000 Subject: gnu: r-affxparser: Update to 1.66.0. * gnu/packages/bioconductor.scm (r-affxparser): Update to 1.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 076bba683c..c054c5bff0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1971,14 +1971,14 @@ CDF file formats.") (define-public r-affxparser (package (name "r-affxparser") - (version "1.64.1") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affxparser" version)) (sha256 (base32 - "0lr0kmp087j2g4i5kd7rh8a038ymp6z82861lyql2fwk5dh80043")))) + "1bd0f8ifj6l7dx2m3wpmd0mji2gdf39mzgcjf9lbvvmbqnbxbcal")))) (properties `((upstream-name . "affxparser"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/affxparser") -- cgit 1.4.1 From eee1bc786a8e2ad923c9267452ed755886a9a541 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:03:58 +0000 Subject: gnu: r-annotate: Update to 1.72.0. * gnu/packages/bioconductor.scm (r-annotate): Update to 1.72.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c054c5bff0..b2110af2dc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1999,14 +1999,14 @@ structure.") (define-public r-annotate (package (name "r-annotate") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 - "13ny596wh65sw7dbw0zd4h84d6k1w99g91c4sqy83mdzgpv73sz7")))) + "0p7q5hdk7003q72vg4hrgdzn463spybxhrkvcq3a6l6jkgy9sf84")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit 1.4.1 From eccd3286842d1114a1604448044e0b65a586ecdf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:03:59 +0000 Subject: gnu: r-annotationdbi: Update to 1.56.1. * gnu/packages/bioconductor.scm (r-annotationdbi): Update to 1.56.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b2110af2dc..1440180c1a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2026,13 +2026,13 @@ microarrays.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.54.1") + (version "1.56.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "0fcammls431pgmp47r85k0zh3bz42bajbqdmafd31kpqncc1ijal")))) + "1svh5zcb7ymz463z5641l2cvzniswxasjjix2plfhqs0yqf1j9qg")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) -- cgit 1.4.1 From 0e31c0034a1fe808255e71c26f1faee45d73db73 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:03:59 +0000 Subject: gnu: r-annotationfilter: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-annotationfilter): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1440180c1a..af755bed6c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2056,13 +2056,13 @@ annotation data packages using SQLite data storage.") (define-public r-annotationfilter (package (name "r-annotationfilter") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFilter" version)) (sha256 (base32 - "0799jja6v7l3jsi26wbjalkr5lriaxid05xb5g36iq93myhaj0sa")))) + "15fp1228yb06jm5cblvhw3qv9mlpbjfggaz2nvi3p46mby1vs64w")))) (properties `((upstream-name . "AnnotationFilter"))) (build-system r-build-system) -- cgit 1.4.1 From c46f29435092fe76c8a76d7fd3a84ed696d08b45 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:03:59 +0000 Subject: gnu: r-annotationforge: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-annotationforge): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index af755bed6c..2a36fbffd5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2082,14 +2082,14 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.34.1") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "0g75b2adak87raw0vn20fjh5980y7svknh8ih1sn4fwryglp4ggg")))) + "02wvni5q560idi6677g5f4md73z4qzjl5yycxv5dbvgbl2picisz")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) -- cgit 1.4.1 From 7f291d0965c1bb0180d090fecfe6d425b97c50e4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:03:59 +0000 Subject: gnu: r-annotationhub: Update to 3.2.0. * gnu/packages/bioconductor.scm (r-annotationhub): Update to 3.2.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2a36fbffd5..79ae4d81e0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2114,14 +2114,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "3.0.2") + (version "3.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "09drr13qqdj7b711axmlxv2gkaw17cvkhl0g2rh7w0b2vx13fg7y")))) + "0ks8yzvvs2r66pb9687mkskf0n3wgvp7h92k83b0a1q32sca5wng")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 9efb70c077b0a746e530819ea43b580c33ee4945 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:03:59 +0000 Subject: gnu: r-aroma-light: Update to 3.24.0. * gnu/packages/bioconductor.scm (r-aroma-light): Update to 3.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 79ae4d81e0..111793874c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2155,14 +2155,14 @@ by the user, helping with quick and reproducible access.") (define-public r-aroma-light (package (name "r-aroma-light") - (version "3.22.0") + (version "3.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aroma.light" version)) (sha256 (base32 - "1yvq6l1p8cpijvlib4fn9y88ihn0gaalrmgx82jgrfmnszkqn3y5")))) + "12qa85hsp8d1xhgn27iymknbhpnp9bd7hsgqxwvp1i8kki06z5hp")))) (properties `((upstream-name . "aroma.light"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From e606add2e4013aff86a3f4f8894866bca586bd1b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:03:59 +0000 Subject: gnu: r-bamsignals: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-bamsignals): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 111793874c..0ffd2efc6b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2182,14 +2182,14 @@ classes.") (define-public r-bamsignals (package (name "r-bamsignals") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bamsignals" version)) (sha256 (base32 - "1ljrip0jlxjcljqac7vzvwqbcqil5v4f4s4bhpq4akvdkshas6mn")))) + "03m3yaagplh7j4q5hp3cfcdqwsnh1pwrlla9cv3ajnfd83s8ncqv")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) -- cgit 1.4.1 From 918c08e20de5fec849377cec52d79407c36f6aa0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:00 +0000 Subject: gnu: r-biobase: Update to 2.54.0. * gnu/packages/bioconductor.scm (r-biobase): Update to 2.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0ffd2efc6b..99f57ef623 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2212,13 +2212,13 @@ paired-end data.") (define-public r-biobase (package (name "r-biobase") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "1sg8w8860zhlz9s1pf75xa8asd2hyqsj13fh5xc37hf5yqdfkavr")))) + "0kar2kgaayp5l7xv9zcxj61l01m8jlwnppql6qf01wsz36dacgww")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) -- cgit 1.4.1 From d0ceaf62fc93e54ed19e723419f0960f8ed37221 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:00 +0000 Subject: gnu: r-biomart: Update to 2.50.0. * gnu/packages/bioconductor.scm (r-biomart): Update to 2.50.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 99f57ef623..fe0ab70b68 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2234,13 +2234,13 @@ on Bioconductor or which replace R functions.") (define-public r-biomart (package (name "r-biomart") - (version "2.48.3") + (version "2.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "096s243yzbhhz3wsm7azml5sznqczmcpi5g0gnb02mah1przczfx")))) + "069wqihm8pj3r41dizvdbj4jnw9bsc5jrz8czfrak5v69bgk5v5q")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) -- cgit 1.4.1 From 7851f7f2c6207ab9d9044f2339250b5c380a5937 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:00 +0000 Subject: gnu: r-biostrings: Update to 2.62.0. * gnu/packages/bioconductor.scm (r-biostrings): Update to 2.62.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fe0ab70b68..e98c88b083 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2327,13 +2327,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.60.2") + (version "2.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "0ai0fg0w4l0a7avbafdbqjgjpg91myxalwrg2i3ixm1l2lyyfyah")))) + "11qkw863mkfz3mc55v2gmfr4w3xziqfb5pq3hmjqpn8vpw8ax3xq")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) -- cgit 1.4.1 From eea602cdbb938e1ae08b5e861d355fff5972ea06 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:00 +0000 Subject: gnu: r-biovizbase: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-biovizbase): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e98c88b083..fdd4e6237d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2355,14 +2355,14 @@ biological sequences or sets of sequences.") (define-public r-biovizbase (package (name "r-biovizbase") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biovizBase" version)) (sha256 (base32 - "14jyyg3ggdhaqhp0j4qf6dapykh76fygbaa4lr7czqbc5mr0iw23")))) + "0kg71p7sqfvxal0c19zrws1ffaqgyi8p605l3z6mkq5ldi26pajz")))) (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From a6b83bd30d115015bf9d20127b7c2c5d0a8d25c0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:00 +0000 Subject: gnu: r-bsgenome: Update to 1.62.0. * gnu/packages/bioconductor.scm (r-bsgenome): Update to 1.62.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fdd4e6237d..e922522304 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2397,13 +2397,13 @@ effort and encourages consistency.") (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "1jhissp9ad1rn2p0bzr3yslbn84yqbaqgnn5p9hyacwr7mr091cn")))) + "1b023dpy8ygq0kd6qy0mk97c66gzpf39y2s0n89kmv61z5sg0jyi")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) -- cgit 1.4.1 From 395e9ab4202520709a84d78b4cc1b8479e33d849 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:00 +0000 Subject: gnu: r-category: Update to 2.60.0. * gnu/packages/bioconductor.scm (r-category): Update to 2.60.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e922522304..0408bd679f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2428,14 +2428,14 @@ genome data packages and support for efficient SNP representation.") (define-public r-category (package (name "r-category") - (version "2.58.0") + (version "2.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "0f76pb7h8qc51mca5pq00m9p02sbkcj6ywfzli20qai2ykpfr71x")))) + "164zp4la9rqnp5vpn2y2p6plc5yxyk2kmn0z3d2flla54zc1b427")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From cd7c1e2c3e8224204125ca0d425280391e04de4f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:01 +0000 Subject: gnu: r-chipseeker: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-chipseeker): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0408bd679f..f44efb6fe5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2459,13 +2459,13 @@ analysis.") (define-public r-chipseeker (package (name "r-chipseeker") - (version "1.28.3") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPseeker" version)) (sha256 (base32 - "18hdgml80770c0xgd06zrl8px1ql9fa65rirfkq07z7rzpnd23rw")))) + "1x8px8ylc231g87rd48kmy9y36h26rldbmqjkcj4mgaldvbsj0rp")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) -- cgit 1.4.1 From 126a4b6c9dafd44e99813440e4ae76c5944f33c6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:01 +0000 Subject: gnu: r-chipseq: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-chipseq): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f44efb6fe5..d4e4f7a727 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2506,14 +2506,14 @@ annotation, distance to TSS, and overlap of peaks or genes.") (define-public r-chipseq (package (name "r-chipseq") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chipseq" version)) (sha256 (base32 - "078p9h0zghlhpd6cr54nww1mk7q97imx8yqfayw5m2yq4097ivbi")))) + "1jw209bfh1c22mqs9z44qx3pmca9m68rhxp0p9bvbmqsnqwrndi6")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) -- cgit 1.4.1 From e5d90645ea046c95536d730713caeca4edcf8e0c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:01 +0000 Subject: gnu: r-complexheatmap: Update to 2.10.0. * gnu/packages/bioconductor.scm (r-complexheatmap): Update to 2.10.0. [propagated-inputs]: Remove r-cairo. --- gnu/packages/bioconductor.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d4e4f7a727..ba498906a1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2532,20 +2532,19 @@ experiments.") (define-public r-complexheatmap (package (name "r-complexheatmap") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ComplexHeatmap" version)) (sha256 (base32 - "0jl96msj1njdrvngg68s50vmphvhi2lfwlv34x07pcdzgkjjs41f")))) + "124w74mk0zk035wyr7cimblzx5blags4n5c8f83mp7iimxcb4gcn")))) (properties `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) (propagated-inputs - `(("r-cairo" ,r-cairo) - ("r-circlize" ,r-circlize) + `(("r-circlize" ,r-circlize) ("r-clue" ,r-clue) ("r-colorspace" ,r-colorspace) ("r-digest" ,r-digest) -- cgit 1.4.1 From f34bcc5c6b3c35b3392a72db3f803c422d36555f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:01 +0000 Subject: gnu: r-copywriter: Update to 2.26.0. * gnu/packages/bioconductor.scm (r-copywriter): Update to 2.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ba498906a1..03d3f2781c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2571,14 +2571,14 @@ self-defined annotation graphics.") (define-public r-copywriter (package (name "r-copywriter") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CopywriteR" version)) (sha256 (base32 - "0pacs714d9b1fdz68pp9ca0x77d376s19lxb82np4l9fgx0rgkxp")))) + "0xm5gjzi4r1xzyn7r669blqxhyhmbk9rh9k2gn696j14hbhc1hcy")))) (properties `((upstream-name . "CopywriteR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 87db919dbb6e67e789581e3b8370d5c8292dbcf0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:01 +0000 Subject: gnu: r-deseq2: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-deseq2): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 03d3f2781c..1efc400e71 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2642,14 +2642,14 @@ distribution.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "0r1brwmj7av0bj72jajn27vx3zs1bgg8qfbhf02fln6kf7im4kaz")))) + "0whk29zrmv9mrlc4w5ghy0fd29v8hfr8jccwgrn59mf3mkmfb2b9")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From cb87707987505aa057138f3fd7ca6858663faa96 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:01 +0000 Subject: gnu: r-dexseq: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-dexseq): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1efc400e71..ba35535bf2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2680,14 +2680,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "1zywh30f4j4rj0f9w6yk5xr9mvdbg8gicy3wsb8yxdnamadyr7x4")))) + "1wd4bjd0a53s689yvb2lxzdiy0synh6ncfcly3cfw37kpdj8lds1")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From de8089a767ba10e6aad736c10f4592f0822e59c2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:02 +0000 Subject: gnu: r-dirichletmultinomial: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-dirichletmultinomial): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ba35535bf2..c8f2443644 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2725,14 +2725,14 @@ exploration of the results.") (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DirichletMultinomial" version)) (sha256 (base32 - "0ikmj0300lfzj6q1vyahfyx5kwi5h59mds7ym4f2j1bbxqzy6ssl")))) + "06nallp9jj2vmaa7d18g6hiymjc109szdv8sp51r87n7s38bvyq6")))) (properties `((upstream-name . "DirichletMultinomial"))) (build-system r-build-system) -- cgit 1.4.1 From 933366ffe74dcf26ac44ffed8794f13c2c98e11d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:02 +0000 Subject: gnu: r-edaseq: Update to 2.28.0. * gnu/packages/bioconductor.scm (r-edaseq): Update to 2.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c8f2443644..a6cc99facd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2754,14 +2754,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-edaseq (package (name "r-edaseq") - (version "2.26.1") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EDASeq" version)) (sha256 (base32 - "0pakcbkalhhqz3d9lpfx3hscf53k24mlmrywxxzfg43yq57srkql")))) + "1vygfdxbjcww7sqzc3j7sp7w13dx10vlzy9z31flf7345qp6blj7")))) (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 46663d57694f2aa977c299fa75d05a298f460fe6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:02 +0000 Subject: gnu: r-edger: Update to 3.36.0. * gnu/packages/bioconductor.scm (r-edger): Update to 3.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a6cc99facd..4283bbd996 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2794,13 +2794,13 @@ global-scaling and full-quantile normalization.") (define-public r-edger (package (name "r-edger") - (version "3.34.1") + (version "3.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "0f6apsjq6cn794840ls9y2n0hix1gyhvkdgxch1v22qr4sq0c86k")))) + "1d18kdfi9vjhhw5kwfy5airrd3c16fh4wbwppbhwgawm038mwavk")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 79736175957a2daa9b672cf6dff4b4505a639098 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:02 +0000 Subject: gnu: r-ensembldb: Update to 2.18.0. * gnu/packages/bioconductor.scm (r-ensembldb): Update to 2.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4283bbd996..9213aa984d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2822,14 +2822,14 @@ CAGE.") (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.16.4") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "15yllkxr6sj5pfvkvv285nk3q5374nzq1iz8ywmnrq910k3xagd8")))) + "02rdbqp33g488w1df1rgp0dg63qrr6w2kmgigxzc8l9wmrvj0y1j")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit 1.4.1 From 309e04ba185ab430221a6717b0a2937f4392cc20 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:02 +0000 Subject: gnu: r-fastseg: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-fastseg): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9213aa984d..58216bed63 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2867,14 +2867,14 @@ chromosome region or transcript models of lincRNA genes.") (define-public r-fastseg (package (name "r-fastseg") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fastseg" version)) (sha256 (base32 - "006v7qs707xmnr35b7rw135pyvacrmhv55a3c53birkpsrjgkps0")))) + "1ds0hhc41nhfj3lmvld8nk2p547wd80b3yq7fjlf3dl3wfaxzy80")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit 1.4.1 From 3a2cab95b1ee615aea4d7e04cb921204fb83b32b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:02 +0000 Subject: gnu: r-gage: Update to 2.44.0. * gnu/packages/bioconductor.scm (r-gage): Update to 2.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 58216bed63..2980c8b69f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2897,14 +2897,14 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.42.0") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "0z7hrwdm6my6p7z04bcpfhqk72pd0s1bdzvsiiym59qj79fbvb83")))) + "1spndmvl8wlz3z3wsvzi0fg9nzk81xi8c220pg2rf81j9181nkar")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit 1.4.1 From 7e80f6fb57e501780e3fa510025393f544a57542 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:02 +0000 Subject: gnu: r-genefilter: Update to 1.76.0. * gnu/packages/bioconductor.scm (r-genefilter): Update to 1.76.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2980c8b69f..b31386d4ad 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2928,14 +2928,14 @@ analysis using other methods.") (define-public r-genefilter (package (name "r-genefilter") - (version "1.74.1") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "0lsh6akhqm1fadxr7066rcx5y7rnd020icx2cq0bfpymz6ajzsvx")))) + "05ba33m99dg414lasn36mjmkd9lvrxgpamy1qj2zvi31i9vkq6y2")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran) -- cgit 1.4.1 From 38d13a6747c3303d1ca14a08425a2ab043cd3693 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:03 +0000 Subject: gnu: r-geneoverlap: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-geneoverlap): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b31386d4ad..974a913d32 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2956,13 +2956,13 @@ high-throughput sequencing experiments.") (define-public r-geneoverlap (package (name "r-geneoverlap") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GeneOverlap" version)) (sha256 (base32 - "1kfw3h68rvbafhklds6sfmviwv91nms8wk0ywzkjg5h3mmgxbsv9")))) + "18l5dc4xcy1xa2h3sfw92w9rq9v0mnclamjxmzs5fqi469y5mwmm")))) (build-system r-build-system) (propagated-inputs `(("r-rcolorbrewer" ,r-rcolorbrewer) -- cgit 1.4.1 From 251e6950d8b65b384d2f3c7dbc13f2bb5fa24123 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:03 +0000 Subject: gnu: r-genomation: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-genomation): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 974a913d32..5a6ab9958e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2976,13 +2976,13 @@ and visualize the results.") (define-public r-genomation (package (name "r-genomation") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "0qa3b4mfd7l1sy4pw64zr2d90y5apah900krxjl4x39acygg0i2r")))) + "0ynwsrlnp98iyz4bl2s7plin0k9iy9zix4jy4v38lcqg6n4iz00j")))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) -- cgit 1.4.1 From 9122892ec962411bebbcd46f1e0fd064a72b7ed7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:03 +0000 Subject: gnu: r-genomeinfodb: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5a6ab9958e..680828f078 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3023,13 +3023,13 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.28.4") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "0fjpgvpvyvl8cqgh2annib6h0c5li3aqz1ajfh5z5k5d0avdm4w0")))) + "1r0wblz9w4hqxm15wdssz0invx7hxhg3bnblkia6w3aazh30s6ns")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) -- cgit 1.4.1 From f599ef1cc4f13bd9e3eb1202b444ce4559d9dc91 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:03 +0000 Subject: gnu: r-genomicalignments: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-genomicalignments): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 680828f078..4f1b6562db 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3053,13 +3053,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "00rq110jkh89nxgk05zh8kssxk8mb4dq0wjg3n7ivfmmm9wdwhp2")))) + "1jwksis94mk8bmdggk0w3kvxqwp4di6x78xgsjk6ij54710adyq9")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) -- cgit 1.4.1 From 60d5b89717a6f2977d4f3b11e1c81948b61c7374 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:03 +0000 Subject: gnu: r-genomicfeatures: Update to 1.46.1. * gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.46.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4f1b6562db..3689377ad3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3086,13 +3086,13 @@ alignments.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.44.2") + (version "1.46.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "091p8xnf2xkqhind81vyv1rmy2fz2b3qalcbrsw4qnp24vgdv2am")))) + "1dm049r7k41m8zzp5b332fw3ah3jpzzgpcb21icxwhlg483ipjyv")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) -- cgit 1.4.1 From 36ea351603d1f90ed5d5e14f1d848ee2e1188529 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:03 +0000 Subject: gnu: r-genomicfiles: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-genomicfiles): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3689377ad3..86fe3a3cac 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3130,14 +3130,14 @@ extracting the desired features in a convenient format.") (define-public r-genomicfiles (package (name "r-genomicfiles") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFiles" version)) (sha256 (base32 - "1plh14m7w6calw5yxcxp7g4bg8q00ax85m517wap78bni975k13y")))) + "0i5y6dk6z18yqj5k4zy756c6l57z9jq2w5a5dksh2di4qgdgjx3x")))) (properties `((upstream-name . "GenomicFiles"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 98c8e7f7356d4889d967c2a3bec0bf799c5368ce Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:04 +0000 Subject: gnu: r-genomicranges: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-genomicranges): Update to 1.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 86fe3a3cac..21026ca4da 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3164,13 +3164,13 @@ provide added flexibility for data combination and manipulation.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "1qxc6dcwdlkan3hg0j9yfhz7gyi9qg671yj6zizsk6mzl7qqva0x")))) + "03fdmzcf8h17ksa3byc3k5mxc65pqrbcnw00myz1q53l01p3cnf2")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) -- cgit 1.4.1 From 8148c6ba72aeb19f640d99126f6289cb8a64e8e3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:04 +0000 Subject: gnu: r-gostats: Update to 2.60.0. * gnu/packages/bioconductor.scm (r-gostats): Update to 2.60.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 21026ca4da..07d3c26672 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3195,14 +3195,14 @@ manipulating genomic intervals and variables defined along a genome.") (define-public r-gostats (package (name "r-gostats") - (version "2.58.0") + (version "2.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOstats" version)) (sha256 (base32 - "0jjswy6qmfgr2f6vk3y9pdvs9x91gn31h55qllgh0qb2cb26g9wa")))) + "1f8wqdl0swnvs59i6ljjcaglfqv314n8zxy4crpx806gbjzpn76z")))) (properties `((upstream-name . "GOstats"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From df5553ee14cc41c1a06898afa67a33908094553f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:04 +0000 Subject: gnu: r-gseabase: Update to 1.56.0. * gnu/packages/bioconductor.scm (r-gseabase): Update to 1.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 07d3c26672..fa0ee907e3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3226,14 +3226,14 @@ testing and other simple calculations.") (define-public r-gseabase (package (name "r-gseabase") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "0946kkykms79mqnx262q20xzrrhv7cv723xh378335ff41qyf63n")))) + "1i8rryvagxk2pd8nl4a6yldwv82yx869nvv95jf8v00bna08f4d6")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From bcd10420ccd61f71638b3ecd201652920a91325d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:04 +0000 Subject: gnu: r-hpar: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-hpar): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fa0ee907e3..ca0c4e47dc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3255,14 +3255,14 @@ Enrichment Analysis} (GSEA).") (define-public r-hpar (package (name "r-hpar") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hpar" version)) (sha256 (base32 - "0q5pp04rq2gsh1kibvp8bvjkqc1kb46qpnj6agqp2vyqhrrfrm99")))) + "1inajapdhjxg0vwhsdnhfq22h3fv7ad7m1lv58y5v41p59av1w76")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) -- cgit 1.4.1 From eeeb38d56919b22395832fc6449c928722a0aa33 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:04 +0000 Subject: gnu: r-rhtslib: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-rhtslib): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ca0c4e47dc..b6cab876d7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3275,14 +3275,14 @@ the Human Protein Atlas project.") (define-public r-rhtslib (package (name "r-rhtslib") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "0acpgv98529ic2i2k03knz05akb6h51wbz7sr5zgi8gk4nmawrlf")))) + "0pwmzwjf6agfp3bq6w8s3piwmzwjdd474qd8zmbzrm772qbadfr4")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) ;; Without this a temporary directory ends up in the Rhtslib.so binary, -- cgit 1.4.1 From b6bd74cefb1057331cac2989f4d31828f883d4e0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:04 +0000 Subject: gnu: r-impute: Update to 1.68.0. * gnu/packages/bioconductor.scm (r-impute): Update to 1.68.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b6cab876d7..34db5f8994 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3306,13 +3306,13 @@ of other R packages who wish to make use of HTSlib.") (define-public r-impute (package (name "r-impute") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "0pprkv25avxhllddcssvqvy3nibmqkfwaq4xnlhka7858gyiyd1k")))) + "0k6dil8ljgp5qr87m7hxli4igb36fbxiwczaqc5pi8mlfh70fqj5")))) (native-inputs `(("gfortran" ,gfortran))) (build-system r-build-system) -- cgit 1.4.1 From 1fa012822dfa84269e477c6c945ca98b5b5f043c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:05 +0000 Subject: gnu: r-interactivedisplaybase: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-interactivedisplaybase): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 34db5f8994..38a8bce27e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3326,14 +3326,14 @@ microarray data, using nearest neighbor averaging.") (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "interactiveDisplayBase" version)) (sha256 (base32 - "00rgrrmglslgb6j7whp0m5dlyl4436r647br05rrpv8cxrmbs2iv")))) + "1pi887192k1jifb4k3pf2jn5hcl1xmmy6vwl22r9njsprdyb3kab")))) (properties `((upstream-name . "interactiveDisplayBase"))) (build-system r-build-system) -- cgit 1.4.1 From a0cc78a554a3666d174c9f45ff47e51b01cae9e4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:05 +0000 Subject: gnu: r-keggrest: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-keggrest): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 38a8bce27e..08b202e311 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3353,14 +3353,14 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "15313d20v3ziyn52fhc6fbzcy1kxjkdx18124bxhdfd14f4aypcd")))) + "1np3i1k7rki9akh70156ggmid52yy0is9q5vd3s45ra7an0ap279")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 0465cc825156f456b57cc5e519e64c29d926dfd5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:05 +0000 Subject: gnu: r-limma: Update to 3.50.0. * gnu/packages/bioconductor.scm (r-limma): Update to 3.50.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 08b202e311..ae0457fce8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3379,13 +3379,13 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-limma (package (name "r-limma") - (version "3.48.3") + (version "3.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "0385ac0hvvml99krcgcpp6q7layjhzgp9xcxkcjrpfg5mjg1z4sx")))) + "05ypmax1s6y1nz42bxn61wxhzzw6185q633crzpdcbbz3dz4vgvy")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") -- cgit 1.4.1 From d4a0101ad96cabe73a7eb674e1493a3ffaf92410 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:05 +0000 Subject: gnu: r-methylkit: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-methylkit): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ae0457fce8..e7c92f2e4d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3398,13 +3398,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-methylkit (package (name "r-methylkit") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "147nag4rz2xpjkkf8rmhja9k4ixjj1hsb0lq3lw7mw6q67zxsvf3")))) + "02px46h2ynprss7kwll3i0jz0clrdg0bys70jacd432xw34nm2sx")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From b96f76aff08fab31e5c0418e7c1e8d1eb9db2d22 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:05 +0000 Subject: gnu: r-mutationalpatterns: Update to 3.4.0. * gnu/packages/bioconductor.scm (r-mutationalpatterns): Update to 3.4.0. [propagated-inputs]: Add r-rcolorbrewer. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e7c92f2e4d..84c8b28177 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3472,14 +3472,14 @@ throughput genetic sequencing data sets using regression methods.") (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") - (version "3.2.0") + (version "3.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 - "0433i4xbz8hrfaj8fxgzps3x8dqrl5vgwzg7qmp4cy5sb1lw5wvs")))) + "1n9rakj57yf17hay1bzvwc2h761yijmlflb3crg1bzwvmn32yhsl")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -3502,6 +3502,7 @@ throughput genetic sequencing data sets using regression methods.") ("r-nmf" ,r-nmf) ("r-pracma" ,r-pracma) ("r-purrr" ,r-purrr) + ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-s4vectors" ,r-s4vectors) ("r-stringr" ,r-stringr) ("r-tibble" ,r-tibble) -- cgit 1.4.1 From 35e1bdc5b88925204bd36ece0a3228cc17b3cb04 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:05 +0000 Subject: gnu: r-msnbase: Update to 2.20.0. * gnu/packages/bioconductor.scm (r-msnbase): Update to 2.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 84c8b28177..e32a6eeaf4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3518,14 +3518,14 @@ in SNV base substitution data.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "1z7s17j6zgb70m0khyf9icqlnbnzlivca7vw7j0vxyw417ld9lkr")))) + "1r5igzb7xb5qcw37ffy0c3j6vlg9zffmksrc57rs1pmfnca773z5")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From a6402a7fee3590ee233ab07dd7d12ff735ff7a5e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:06 +0000 Subject: gnu: r-msnid: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-msnid): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e32a6eeaf4..e81a31e3f7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3563,14 +3563,14 @@ of mass spectrometry based proteomics data.") (define-public r-msnid (package (name "r-msnid") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "0r3vgigf4fk0xzfg8gcvad01jdh0fysh6x22m9qy77x6glyrxcj2")))) + "0dks5h3vp9ly8x24px2rl5blqicxybpxjnxvg2p1bwq8zvjkm38p")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (arguments -- cgit 1.4.1 From 62d157a2e2194cafc69ca2837de80b14e48023bc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:06 +0000 Subject: gnu: r-mzid: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-mzid): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e81a31e3f7..3aa05ba4dc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3620,14 +3620,14 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-mzid (package (name "r-mzid") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 - "1wsy6frxa5602jqb1nlqv39mzgpid8wfyvb9m2jb6srv7p59rgys")))) + "0r001amd4m99cv0ixw38rpz0zv0xqb0qyvs16bz1i4a756391qri")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 3de4beb0133dda64ed759b11da50c49666d47d53 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:06 +0000 Subject: gnu: r-mzr: Update to 2.28.0. * gnu/packages/bioconductor.scm (r-mzr): Update to 2.28.0. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3aa05ba4dc..b20668a57a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3651,14 +3651,14 @@ specific parser.") (define-public r-mzr (package (name "r-mzr") - (version "2.26.1") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "0z4cz6lir9gwzy0hxwv03wv36fkkfdb97p9wv4af020k0zkp3ipr")) + "1azq0wjjy6n5xc721gjz6afm43ajz15b4p34vgsdjzwg9qn1vrs1")) (modules '((guix build utils))) (snippet '(begin @@ -3681,7 +3681,7 @@ specific parser.") #t))))) (inputs `(;; Our default boost package won't work here, unfortunately, even with - ;; mzR version 2.26.1. + ;; mzR version 2.28.0. ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources ("zlib" ,zlib))) (propagated-inputs -- cgit 1.4.1 From ada8646a38bd67ec5b098e5b9ce44e6b68e0862d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:06 +0000 Subject: gnu: r-organismdbi: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-organismdbi): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b20668a57a..308c85420d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3708,14 +3708,14 @@ previously been used in XCMS.") (define-public r-organismdbi (package (name "r-organismdbi") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OrganismDbi" version)) (sha256 (base32 - "0p8ccpdchdwci4kv9y07wdadzgms8nipvg6rm1rll35jcflnnkxi")))) + "0zp6x2iqhn9s3xp07yilnr6hn73acvkdai5xip4iiwjdlnfffj83")))) (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 78fd7685668c1846792496b624bbbc3baeebf46e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:06 +0000 Subject: gnu: r-pcamethods: Update to 1.86.0. * gnu/packages/bioconductor.scm (r-pcamethods): Update to 1.86.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 308c85420d..e61b7b8811 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3740,14 +3740,14 @@ the fact that each of these packages implements a select methods.") (define-public r-pcamethods (package (name "r-pcamethods") - (version "1.84.0") + (version "1.86.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaMethods" version)) (sha256 (base32 - "1ccqsxn487dy92c2d1iffh9917z4zq5ia92zv2h6pi00jjc6ymb5")))) + "1fj2v6sna4lbw7ar9h93y2g4pzylqqp7760ih425gcai7s19xdrg")))) (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From dc4cc2aa3223a1cc48f0a6ff9516dd392447d093 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:06 +0000 Subject: gnu: r-protgenerics: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-protgenerics): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e61b7b8811..a9ccd9a824 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3770,14 +3770,14 @@ structure (pcaRes) to provide a common interface to the PCA results.") (define-public r-protgenerics (package (name "r-protgenerics") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ProtGenerics" version)) (sha256 (base32 - "1c79k8nc28782w5gxi7pkm8jmddq1hdw6khs9kgsp8dyk60ak6fq")))) + "0x53pk7h47gjza1q5pz7jb1qqhwa9z2rr5fr61qc92zl3mqk57m0")))) (properties `((upstream-name . "ProtGenerics"))) (build-system r-build-system) (home-page "https://github.com/lgatto/ProtGenerics") -- cgit 1.4.1 From 3caf93321d4dc2b9f5db927ea323f277e435e874 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:07 +0000 Subject: gnu: r-rbgl: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-rbgl): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a9ccd9a824..cb5405174e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3790,14 +3790,14 @@ proteomics packages.") (define-public r-rbgl (package (name "r-rbgl") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 - "0l40ibf8g5s4ay83s92l198jjqc5l09hcmxqcjrpifvp5pjf9yy5")))) + "0k2p1lwdvix4n742a97lv988rx5kg8cvcmzgyzj0538n1nz0lxk0")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From c4908b9effbf6aa8401e182963cba2c7adb47f35 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:07 +0000 Subject: gnu: r-rcas: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-rcas): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cb5405174e..162d1e1134 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3813,13 +3813,13 @@ the graph algorithms contained in the Boost library.") (define-public r-rcas (package (name "r-rcas") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RCAS" version)) (sha256 (base32 - "0l92v870ndna8zjqwzf22fb9vyhkh6942v4gaiqr1yc4qr521p5p")))) + "02zwz7c8ljmdcfxj54xns0a31sj616x63q63wxhxa1nb4dhgmvk7")))) (properties `((upstream-name . "RCAS"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From cbf8dbc3cb3d35b9c52bc98c7666800b74dc2df6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:07 +0000 Subject: gnu: r-regioner: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-regioner): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 162d1e1134..feb074e703 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3863,14 +3863,14 @@ library implementing most of the pipeline's features.") (define-public r-regioner (package (name "r-regioner") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "0xzzaz3cl6pyxfsg0d931v8k15wbd05s5mnsb7igxldc5qqg3nsl")))) + "0y1mawzfvxrympc47q3isk96sl9d1bc8kdsxpm8rnhqg5bmgwya6")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 559953466ed705df009d1c0e5a476ea730965847 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:07 +0000 Subject: gnu: r-reportingtools: Update to 2.34.0. * gnu/packages/bioconductor.scm (r-reportingtools): Update to 2.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index feb074e703..019fcbfa18 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3894,14 +3894,14 @@ region sets and other genomic features.") (define-public r-reportingtools (package (name "r-reportingtools") - (version "2.32.1") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReportingTools" version)) (sha256 (base32 - "0wq9y649dh1am6djzz0xlz42428xsgw2bdx1dknhdw2xbydmmx47")))) + "06kwf87h84xgswkrm7brmgr9aj1nf6cxp24hrfymkzq2pha5y5j7")))) (properties `((upstream-name . "ReportingTools"))) (build-system r-build-system) -- cgit 1.4.1 From 148e520d4aaaeb797e9561e9ea91857d73910a42 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:07 +0000 Subject: gnu: r-rhdf5: Update to 2.38.0. * gnu/packages/bioconductor.scm (r-rhdf5): Update to 2.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 019fcbfa18..7cb45da1eb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3944,13 +3944,13 @@ browser.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "1a5kw9ry9cr258al0x3q0ss5xn1ymscdypx51vzzgzamhy7dqakz")))) + "13zm993l3i9f98gqdpxgsrzf9fgqppx2ajvrl0i3f7cvpifcgxqg")))) (build-system r-build-system) (propagated-inputs `(("r-rhdf5filters" ,r-rhdf5filters) -- cgit 1.4.1 From e38d61947663ab03c4b551a24aeb29fd784adaf4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:07 +0000 Subject: gnu: r-rhdf5filters: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-rhdf5filters): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7cb45da1eb..6e7d14afcc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3972,14 +3972,14 @@ the available RAM.") (define-public r-rhdf5filters (package (name "r-rhdf5filters") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5filters" version)) (sha256 (base32 - "133v0s452acspi4dbf6gsa2xrr0qza86jdjjbpwhdv6zfd1djbgc")))) + "05b015pyp3g1crmm2d3ldsa7r5w0khmf87qbl4fv16r6pdggha78")))) (properties `((upstream-name . "rhdf5filters"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From f0774df7c13c53a994b90587f986ecbb5ecf4fda Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:08 +0000 Subject: gnu: r-rsamtools: Update to 2.10.0. * gnu/packages/bioconductor.scm (r-rsamtools): Update to 2.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6e7d14afcc..f64d1875f4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3998,13 +3998,13 @@ HDF5 datasets.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "0arhh5bbx3pmxmkh5sjgczcswqy83d35r7cjhd2knpczdvrixaq5")))) + "0v6b3j45ivd9f04fpfs1vjwby5pi30mf5683bjxim01vi2krj9yh")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) -- cgit 1.4.1 From d076801410854e42d7e2c7ff686357f80480b1df Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:08 +0000 Subject: gnu: r-rtracklayer: Update to 1.54.0. * gnu/packages/bioconductor.scm (r-rtracklayer): Update to 1.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f64d1875f4..d2abb0f964 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4067,13 +4067,13 @@ tab-delimited (tabix) files.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.52.1") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "11w6dx09pb49lin1gr9q88xn7ixh9jd5z6m9z27djchm0nw10lx9")))) + "11bh9khra2qdmicppi6ya43kf8f1z13ak92vkl6nr5f20k54cphc")))) (build-system r-build-system) (arguments `(#:phases -- cgit 1.4.1 From 09d921d4421b8e19612e661ce76eb9248ce7dbf8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:08 +0000 Subject: gnu: r-seqlogo: Update to 1.60.0. * gnu/packages/bioconductor.scm (r-seqlogo): Update to 1.60.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d2abb0f964..77329a81dd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4146,14 +4146,14 @@ differential expression analysis, RNAseq data and related problems.") (define-public r-seqlogo (package (name "r-seqlogo") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqLogo" version)) (sha256 (base32 - "1253sj1hc6bbrff0iv5xa3v9znqvisll0fy6fdjka9c778fn4mcp")))) + "013hwj2lp29nqa8mkvm25aliarg0k725crg4cpsbj0iiskyrs6rl")))) (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) (native-inputs -- cgit 1.4.1 From f1dedc13dcdd6e5295e2be15596b0ee8bcdc0559 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:08 +0000 Subject: gnu: r-seqpattern: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-seqpattern): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 77329a81dd..86e0c0583d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4169,13 +4169,13 @@ Stephens (1990).") (define-public r-seqpattern (package (name "r-seqpattern") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqPattern" version)) (sha256 (base32 - "0h74z84zyvfzclsm0g13b95hirn99185wc6lp53jkzah9yyi59ay")))) + "1mik575qaxw9h9qyjn971207pfgbc8p1mx60jrb20jbrrihgg2na")))) (properties `((upstream-name . "seqPattern"))) (build-system r-build-system) -- cgit 1.4.1 From bf90dbefccdff3133b4a446a26d8eda6ac309d33 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:08 +0000 Subject: gnu: r-shortread: Update to 1.52.0. * gnu/packages/bioconductor.scm (r-shortread): Update to 1.52.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 86e0c0583d..b92e51afa7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4196,14 +4196,14 @@ reference point and sorted by a user defined feature.") (define-public r-shortread (package (name "r-shortread") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "0zqinw3c6h5v1c5nhzkiziirws16nbviccgw8nj2d22r33dbqwp3")))) + "1p17v15wd3v6w9ligpjjk28vy8k2ql57y2hhm8y6vnv9y3nagjsx")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs -- cgit 1.4.1 From 9398e3e047399030af75306be6f79695414d18a6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:08 +0000 Subject: gnu: r-simplifyenrichment: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-simplifyenrichment): Update to 1.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b92e51afa7..dff52e6b13 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4239,14 +4239,14 @@ ungapped alignment formats.") (define-public r-simplifyenrichment (package (name "r-simplifyenrichment") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "simplifyEnrichment" version)) (sha256 (base32 - "0rqa414kvyjjmj4932zk39rqa14z13b57rkrxdrf16jmq2r437vh")))) + "05d9yjd8s7q1q78qmnx5xfrz9ppswc2cpfmjj47d338w783lwk98")))) (properties `((upstream-name . "simplifyEnrichment"))) (build-system r-build-system) -- cgit 1.4.1 From 91c78f9527ac121ebc421756e6afbf7fb49ed584 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:08 +0000 Subject: gnu: r-trajectoryutils: Update to 1.2.0. * gnu/packages/bioconductor.scm (r-trajectoryutils): Update to 1.2.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dff52e6b13..f4be95c14e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4278,14 +4278,14 @@ and comparing the clusterings.") (define-public r-trajectoryutils (package (name "r-trajectoryutils") - (version "1.0.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TrajectoryUtils" version)) (sha256 (base32 - "1b7mg3ypp1ay98cav47h9vn692lx0n9b5b0hpansgnkr5prb823b")))) + "0pzm1h69bg04a2v09r8c6pb3pix6f3n5dylvbv7wsp574qfaqyd1")))) (properties `((upstream-name . "TrajectoryUtils"))) (build-system r-build-system) -- cgit 1.4.1 From 41e1bf39aa6c04b32d170448b1537c0374787af7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:09 +0000 Subject: gnu: r-slingshot: Update to 2.2.0. * gnu/packages/bioconductor.scm (r-slingshot): Update to 2.2.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f4be95c14e..93eb2c5e11 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4308,13 +4308,13 @@ structures to hold pseudotime inference results.") (define-public r-slingshot (package (name "r-slingshot") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "slingshot" version)) (sha256 (base32 - "1aqsz2kxwax8d8d5iv3zk5hlyk5aya1wbxs1wky2rgccw4d35whx")))) + "081kp9b0lpw2xq9xvd2kykqqrqcj322mp7xa44xc3kf0nzsivqfa")))) (build-system r-build-system) (propagated-inputs `(("r-igraph" ,r-igraph) -- cgit 1.4.1 From 2a3f2f002e61ec2014969ab22ef4ec656ac97d1b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:09 +0000 Subject: gnu: r-structuralvariantannotation: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-structuralvariantannotation): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 93eb2c5e11..129dc2f54a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4340,13 +4340,13 @@ graph construction.") (define-public r-structuralvariantannotation (package (name "r-structuralvariantannotation") - (version "1.8.2") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "StructuralVariantAnnotation" version)) (sha256 - (base32 "04ac4mjh3pgdlws0aiacqg0vd7bhg890w44r7b90p947c3rk1mfw")))) + (base32 "1pw7d39944dwk5gw6q7igcn866zpqwz01ljaha2ih5dfvmhxka8n")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) -- cgit 1.4.1 From 679abce085b3db1410efe274c8853f6d7ee70d64 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:09 +0000 Subject: gnu: r-summarizedexperiment: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-summarizedexperiment): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 129dc2f54a..bf1f519788 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4377,13 +4377,13 @@ involving two separate genomic loci encoded as GRanges objects.") (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "16np5ik6jgbi68mhlib6yskywwbaa50mlr7m3sh1hqk889whfn1g")))) + "0qpnx2aii9vs7fcp0ax5j77ysbhi4qhjhm35vnygs3isbrjn925a")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) -- cgit 1.4.1 From c3d9b4b0979d99d07599d3738ddfb78fca018fa1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:09 +0000 Subject: gnu: r-sva: Update to 3.42.0. * gnu/packages/bioconductor.scm (r-sva): Update to 3.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bf1f519788..b7b1b6ae9a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4411,14 +4411,14 @@ samples.") (define-public r-sva (package (name "r-sva") - (version "3.40.0") + (version "3.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "12jkcybdfspabh7x124d44l9fj1hwwg3gvcqxvz5wpkiflc2vkji")))) + "0clzid9di2qfgc5bvnqx312k3inj1lc599ckqkllvr894wxb7mdj")))) (build-system r-build-system) (propagated-inputs `(("r-edger" ,r-edger) -- cgit 1.4.1 From 442a35502678c50acdf37fec875b5103d9f2bd8b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:09 +0000 Subject: gnu: r-systempiper: Update to 2.0.0. * gnu/packages/bioconductor.scm (r-systempiper): Update to 2.0.0. [propagated-inputs]: Remove r-annotate, r-assertthat, r-batchtools, r-deseq2, r-dot, r-edger, r-genomicfeatures, r-go-db, r-gostats, r-iranges, r-limma, r-pheatmap, r-rjson, r-rsvg, r-testthat, and r-variantannotation; add r-biocgenerics and r-htmlwidgets. --- gnu/packages/bioconductor.scm | 24 +++++------------------- 1 file changed, 5 insertions(+), 19 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b7b1b6ae9a..f04e96c23a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4442,44 +4442,30 @@ unmodeled, or latent sources of noise.") (define-public r-systempiper (package (name "r-systempiper") - (version "1.26.3") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "01l35l5zj87qkarrbal9la6kshk3j7k8hy3iimv3gdnnz4axmvs7")))) + "0kibr47z7ml13hpl955qcr4wp2z4nq7gjiinyk30wivrwrng5sg1")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-assertthat" ,r-assertthat) - ("r-batchtools" ,r-batchtools) + `(("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) ("r-crayon" ,r-crayon) - ("r-deseq2" ,r-deseq2) - ("r-dot" ,r-dot) - ("r-edger" ,r-edger) - ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) - ("r-go-db" ,r-go-db) - ("r-gostats" ,r-gostats) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) + ("r-htmlwidgets" ,r-htmlwidgets) ("r-magrittr" ,r-magrittr) - ("r-pheatmap" ,r-pheatmap) - ("r-rjson" ,r-rjson) ("r-rsamtools" ,r-rsamtools) - ("r-rsvg" ,r-rsvg) ("r-s4vectors" ,r-s4vectors) ("r-shortread" ,r-shortread) ("r-stringr" ,r-stringr) ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-testthat" ,r-testthat) - ("r-yaml" ,r-yaml) - ("r-variantannotation" ,r-variantannotation))) + ("r-yaml" ,r-yaml))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/tgirke/systemPipeR") -- cgit 1.4.1 From bb69853f898909e114c70bee30d5634f39278827 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:09 +0000 Subject: gnu: r-topgo: Update to 2.46.0. * gnu/packages/bioconductor.scm (r-topgo): Update to 2.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f04e96c23a..940c307d3e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4485,13 +4485,13 @@ annotation infrastructure.") (define-public r-topgo (package (name "r-topgo") - (version "2.44.0") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "1ggi7yrhkyi85p3sfj3yd95n9mzq1xpff28ixa4dl9yzasks1v5a")))) + "01vykf8bzwm2k7cfj09r6il6qaycjy10wpaxbn13f21p66r5nlm2")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) -- cgit 1.4.1 From 47c3ec038e503746992006d9b512633af5825972 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:10 +0000 Subject: gnu: r-tximport: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-tximport): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 940c307d3e..9cdb8f9b06 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4518,13 +4518,13 @@ dependencies between GO terms can be implemented and applied.") (define-public r-tximport (package (name "r-tximport") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "0ip2yr0zspf2aagskxl4dwncr48dw5qb90an3sswnnh2dqdb82if")))) + "0w6pr7s9j8l4fpn3przbfrsyxvzxc3ficgsychvhq3bami9np8g4")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) -- cgit 1.4.1 From e1743135414872f1e26688c9d137b7edcab81d29 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:10 +0000 Subject: gnu: r-variantannotation: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-variantannotation): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9cdb8f9b06..287b024e5d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4542,13 +4542,13 @@ of gene-level counts.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "0c9r00j8a3bs6n0dv4wi17jc1ljzvr3r2bi4h9axhcsf2ip906rh")))) + "1r9kayp0hxcwls08lv2fh0cmf9ks0lqx3k31c1zn4asw4dyqpgva")))) (properties `((upstream-name . "VariantAnnotation"))) (propagated-inputs -- cgit 1.4.1 From 0b341967e3b950c21552b95213bdf0257d9632fc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:10 +0000 Subject: gnu: r-vsn: Update to 3.62.0. * gnu/packages/bioconductor.scm (r-vsn): Update to 3.62.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 287b024e5d..d43bb759ed 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4580,14 +4580,14 @@ coding changes and predict coding outcomes.") (define-public r-vsn (package (name "r-vsn") - (version "3.60.0") + (version "3.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "vsn" version)) (sha256 (base32 - "0nppph3kv8z83368snb8s3n4vcqj829yyi1kh4q09qvq18rhvssv")))) + "03p2wdjbjnrn1ddyz0fbn04mdxpsmv83qhh3apj6azshl0bs1j2x")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) -- cgit 1.4.1 From 469cf86fa2133915d62d0c889ea677df06554a75 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:10 +0000 Subject: gnu: r-xvector: Update to 0.34.0. * gnu/packages/bioconductor.scm (r-xvector): Update to 0.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d43bb759ed..d612f4ceb7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4616,13 +4616,13 @@ and specific in detecting differential transcription.") (define-public r-xvector (package (name "r-xvector") - (version "0.32.0") + (version "0.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 - "1cw34gd9iaspl0v737xl7rngq63zrj03a5ngai15ggrnv1sq2aqr")))) + "07r4qgmnifw9jk2srjg0cvl310j0f9y35jrg0zqhlvhmyhg6n2c0")))) (properties `((upstream-name . "XVector"))) (build-system r-build-system) -- cgit 1.4.1 From c3a3c417c07b773f9a20d69bce088ebdec5fd806 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:10 +0000 Subject: gnu: r-zlibbioc: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-zlibbioc): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d612f4ceb7..d9bf128d59 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4652,13 +4652,13 @@ and specific in detecting differential transcription.") (define-public r-zlibbioc (package (name "r-zlibbioc") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zlibbioc" version)) (sha256 (base32 - "1dv5bf12kzk1yzyfs3g5syim16sbi44kalvzj2i2xcnxnl6x60ip")))) + "0a0dl7z58zxdj6938zbxixphgljj1giylk1nd05bb7qsccmp0xhj")))) (properties `((upstream-name . "zlibbioc"))) (build-system r-build-system) -- cgit 1.4.1 From 319038ace30e2b9cf5ff320704be218495e77d22 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:10 +0000 Subject: gnu: r-geneplotter: Update to 1.72.0. * gnu/packages/bioconductor.scm (r-geneplotter): Update to 1.72.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d9bf128d59..1840f8b166 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4703,14 +4703,14 @@ saving AnnData objects to disk.") (define-public r-geneplotter (package (name "r-geneplotter") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneplotter" version)) (sha256 (base32 - "1d085lfa3yif5wkys1fb0zzgg0cqwd1y18vasgqqdr6rva075d4z")))) + "1b7ngp9l00vrymx3d3nsda546s7p4ifr90idn3x2v4ilf38rfhp8")))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) -- cgit 1.4.1 From 0cffd1577158ee0a5650371b871b8d96fb7a8e06 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:11 +0000 Subject: gnu: r-oligoclasses: Update to 1.56.0. * gnu/packages/bioconductor.scm (r-oligoclasses): Update to 1.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1840f8b166..9229c93ae5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4728,14 +4728,14 @@ saving AnnData objects to disk.") (define-public r-oligoclasses (package (name "r-oligoclasses") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligoClasses" version)) (sha256 (base32 - "1nsfyfpj264h6y322pzz0i001b0m862j3skbq5rjwlrj1p8j2gi7")))) + "1ia2f19swiwb0552nfwkai4gl0av07cj75b6jwiviqa1bli09264")))) (properties `((upstream-name . "oligoClasses"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 980a36cbeea9b25b46a3be5c37db999cfda0157d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:11 +0000 Subject: gnu: r-oligo: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-oligo): Update to 1.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9229c93ae5..0b79e22e02 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4763,14 +4763,14 @@ packages.") (define-public r-oligo (package (name "r-oligo") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligo" version)) (sha256 (base32 - "0fyq77im6s79havjwbchhqhnllxs134jsi98g6msxz66h16lj3al")))) + "1cmnnq0d5xsjsx8c8n8wcl6l9d31sbglb8yrsibykcvnhw15fsf6")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) -- cgit 1.4.1 From c6c1f9fc72dc4ad1bedd5726a9ee01f2ca369744 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:11 +0000 Subject: gnu: r-qvalue: Update to 2.26.0. * gnu/packages/bioconductor.scm (r-qvalue): Update to 2.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0b79e22e02..42336e69b1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4799,14 +4799,14 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).") (define-public r-qvalue (package (name "r-qvalue") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 - "0xssanffh1hr7f48mnazcpwi25rdp7mxlyb9nbf4q2mp7m40jnpm")))) + "1mn2qmqn89lfsx7rg54d1lwz45bfx0b91q6ahf43a1yzrrhwn138")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) -- cgit 1.4.1 From 88c203a85fab5ea4361fa7a60f1f4833a27c525e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:11 +0000 Subject: gnu: r-apeglm: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-apeglm): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 42336e69b1..c0d9f16dcb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4854,13 +4854,13 @@ integration with @code{Rcpp}.") (define-public r-apeglm (package (name "r-apeglm") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "apeglm" version)) (sha256 (base32 - "1xld6ar440achik4dbd7vhiw6jfj0sb96jm52n7hav5bv4gag3mh")))) + "11w4vyc1sllmm5lh42krhidazid78n4s3lhikpy9kk2l57jmifbr")))) (properties `((upstream-name . "apeglm"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From d05485f7f74f7510f96d2173f1fa431c7ae3e079 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:11 +0000 Subject: gnu: r-greylistchip: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-greylistchip): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c0d9f16dcb..9b0aa18172 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4881,13 +4881,13 @@ posterior for individual coefficients.") (define-public r-greylistchip (package (name "r-greylistchip") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GreyListChIP" version)) (sha256 (base32 - "1g9ja8p90czx83ar0l9ran7m6aggvszdbqm714fq7z4rxq9b4hs3")))) + "1h7h27q6l9d8j0shklyrh135zrwx56v4zzmm21cj1b7dvmwvpbcv")))) (properties `((upstream-name . "GreyListChIP"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 6f6478b175c9224bcbaa8eaad0a75b9c6aec90e1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:11 +0000 Subject: gnu: r-diffbind: Update to 3.4.0. * gnu/packages/bioconductor.scm (r-diffbind): Update to 3.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9b0aa18172..f9f1bbb73c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4908,14 +4908,14 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "3.2.7") + (version "3.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "01jfxcj5c0088vvsi3pz8fs0ka6n12l2j8s1d0rpqwa1y0444x7z")))) + "15p4jd9k520va6kzizkgsl4a18kh5r8i50qfdkv7xazsfhvxjm3i")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 8826132332df7494cf3ad5812854039142852b52 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:12 +0000 Subject: gnu: r-mbkmeans: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-mbkmeans): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f9f1bbb73c..eb37dc0043 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4986,13 +4986,13 @@ processing to visualization and annotation.") (define-public r-mbkmeans (package (name "r-mbkmeans") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mbkmeans" version)) (sha256 (base32 - "1k7ngpx4s50jplrsv19zzjr7izpdl9wwppb218ih5cp0ki1gcc2n")))) + "03hpj218s8fynmk1s50s0rinhsljikxdrff06yc8ysbyc6hyfb4k")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) -- cgit 1.4.1 From d6a3debb6d57494e3c6780228edb7703a7b59c04 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:12 +0000 Subject: gnu: r-multtest: Update to 2.50.0. * gnu/packages/bioconductor.scm (r-multtest): Update to 2.50.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index eb37dc0043..509b4b7c14 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5018,14 +5018,14 @@ large datasets, including support for on-disk data representation.") (define-public r-multtest (package (name "r-multtest") - (version "2.48.0") + (version "2.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "multtest" version)) (sha256 (base32 - "1wi15v4llgv11hpb2j9h4a35nrnawnmvbz5d5dvgy8lhqrlq8w9a")))) + "03z71r7g318nwwgiz0k8qwbhghw1hhdhh1an4qnb0nc62c5x9kns")))) (build-system r-build-system) (propagated-inputs `(("r-survival" ,r-survival) -- cgit 1.4.1 From aad12099dd007fc11734b5041b087b39f5ab5446 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:12 +0000 Subject: gnu: r-graph: Update to 1.72.0. * gnu/packages/bioconductor.scm (r-graph): Update to 1.72.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 509b4b7c14..67769dc584 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5056,13 +5056,13 @@ expressed genes in DNA microarray experiments.") (define-public r-graph (package (name "r-graph") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 - "1i7s198d5kw4gk6nqqsd3vqaknj4493p822f2za8q95gv6x02rxa")))) + "0x31lz3qimxmng6w99xnqazaj943d94b04nbziad4jfv7c1bc2h0")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics))) -- cgit 1.4.1 From 0d11010cef0c7d9a0d27c02feaea91a6c6139fc1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:12 +0000 Subject: gnu: r-chippeakanno: Update to 3.28.0. * gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 67769dc584..eed51549f7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5154,14 +5154,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.26.4") + (version "3.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "1iqzm7pifl9zrw3s06i6h85n1p01pd06vh1a93izyfhgybxn262d")))) + "05fbq8zvww1nlyykrri0hf4248i1i7w5cr453giagmjq7lgg4v3b")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 7bda0a92208b8bd94215227a67361b44d2ce6c02 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:12 +0000 Subject: gnu: r-matrixgenerics: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-matrixgenerics): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index eed51549f7..218150cb36 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5208,13 +5208,13 @@ enrichedGO (addGeneIDs).") (define-public r-matrixgenerics (package (name "r-matrixgenerics") - (version "1.4.3") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MatrixGenerics" version)) (sha256 (base32 - "1yir3rwhz5vf0pdn3fpvlc57c75k98gvv8gapajbvymz3lyghijv")))) + "1s75p8rrmj24r0vcbaiyw8xg8y84j388mv6iawai7pypfcl8s1z3")))) (properties `((upstream-name . "MatrixGenerics"))) (build-system r-build-system) -- cgit 1.4.1 From c6cff9686b61434087c2cb1dfe4496a3ed01b530 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:12 +0000 Subject: gnu: r-marray: Update to 1.72.0. * gnu/packages/bioconductor.scm (r-marray): Update to 1.72.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 218150cb36..48b250c2f9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5235,12 +5235,12 @@ incompatibilities.") (define-public r-marray (package (name "r-marray") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "marray" version)) (sha256 - (base32 "0wpmrhqpyv27h1hn31hzz21r74r7yqx79ljv8i8gn6ix8lf5ca56")))) + (base32 "1la805y8j522vpiazm1z6wpq4ibia9bib5fpiia5mxmpzmqg6gzz")))) (build-system r-build-system) (propagated-inputs `(("r-limma" ,r-limma))) -- cgit 1.4.1 From c5cb1e01181203bf8223a32ff1b92097c0a36d38 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:12 +0000 Subject: gnu: r-cghbase: Update to 1.54.0. * gnu/packages/bioconductor.scm (r-cghbase): Update to 1.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 48b250c2f9..23116cb251 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5254,12 +5254,12 @@ normalization and quality checking.") (define-public r-cghbase (package (name "r-cghbase") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHbase" version)) (sha256 - (base32 "1p87k4vw981k97d9bckmprrfg55jwd91658rgxzjj8hnschf28a4")))) + (base32 "1kfxw126bddfy67cmf8dca9qq4bg7fkxjf8iaikplhvs5hl7bp4d")))) (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 19fb6bae8ce6969669ac20040ee8abbe59e8e9aa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:13 +0000 Subject: gnu: r-cghcall: Update to 2.56.0. * gnu/packages/bioconductor.scm (r-cghcall): Update to 2.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 23116cb251..31a7764909 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5274,12 +5274,12 @@ the @code{arrayCGH} packages.") (define-public r-cghcall (package (name "r-cghcall") - (version "2.54.0") + (version "2.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHcall" version)) (sha256 - (base32 "1zik04y2q0anzy85l0b4ryzkxpfx2fnmpwp5s7akyk1jfl2r8gw7")))) + (base32 "1r4y8zakgmdbnpwgp14kwh4iwqgqcmjq2yg4nc7j37p09bw1c8zr")))) (properties `((upstream-name . "CGHcall"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 29bfd56aa0261449a931b50981d0c9780f7a03f0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:13 +0000 Subject: gnu: r-qdnaseq: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-qdnaseq): Update to 1.30.0. [propagated-inputs]: Remove r-future. --- gnu/packages/bioconductor.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 31a7764909..63f4f9aa52 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5297,12 +5297,12 @@ the @code{arrayCGH} packages.") (define-public r-qdnaseq (package (name "r-qdnaseq") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QDNAseq" version)) (sha256 - (base32 "1p4544xlarkbgs9kybrrawq3v7qr6ix62nrc6l7dcksh2ka69yzf")))) + (base32 "1sza9br8agpdz1k9fn5wisir44sj8v0rk4wbx35d2c2kp9q70pqj")))) (properties `((upstream-name . "QDNAseq"))) (build-system r-build-system) (propagated-inputs @@ -5310,7 +5310,6 @@ the @code{arrayCGH} packages.") ("r-cghbase" ,r-cghbase) ("r-cghcall" ,r-cghcall) ("r-dnacopy" ,r-dnacopy) - ("r-future" ,r-future) ("r-future-apply" ,r-future-apply) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) -- cgit 1.4.1 From f1cc3281015a8f541dfcd23e20f8e144ddf96a22 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:13 +0000 Subject: gnu: r-bayseq: Update to 2.28.0. * gnu/packages/bioconductor.scm (r-bayseq): Update to 2.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 63f4f9aa52..0408feeae8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5329,14 +5329,14 @@ respectively.") (define-public r-bayseq (package (name "r-bayseq") - (version "2.26.0") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "baySeq" version)) (sha256 (base32 - "0hyc0sl2nf18bz0jxbzim0v41zwh2rnnr7l3p6zkk9wnw5gn7bbc")))) + "1zgxwb287ccz4wqsjxmffknnzziv12l4yrw7df912dxz6yccvd8r")))) (properties `((upstream-name . "baySeq"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 4f094515b031e3a343b020c4c81db92234e025a7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:13 +0000 Subject: gnu: r-chipcomp: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-chipcomp): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0408feeae8..c7dbfcb5a6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5355,14 +5355,14 @@ more complex hypotheses) via empirical Bayesian methods.") (define-public r-chipcomp (package (name "r-chipcomp") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPComp" version)) (sha256 (base32 - "1kfxjh1mynrgqsy2q6byf03cbymqc8w7l7672iyd0wj5qzlif4h5")))) + "1wdy92y5l3wa3zgg59w69rd7gdwf4z1waa4i2cccniccz463p1xq")))) (properties `((upstream-name . "ChIPComp"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 765052f5dc42f1e063bca256211b802e9c4e2073 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:13 +0000 Subject: gnu: r-riboprofiling: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-riboprofiling): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c7dbfcb5a6..8968e15b45 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5389,14 +5389,14 @@ datasets.") (define-public r-riboprofiling (package (name "r-riboprofiling") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RiboProfiling" version)) (sha256 (base32 - "1jmd8yrv7p7hn4gdibg3svmhqxjyrnfp7cgsqg8zv862lgd75zsl")))) + "1szlzvm8ggjc40k4z2fxxa2h28g6j9wj2g5aw480v9hgyvvdw5lx")))) (properties `((upstream-name . "RiboProfiling"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 56da30065a38b8aad1b9099b1a91db11b088bb47 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:13 +0000 Subject: gnu: r-riboseqr: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-riboseqr): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8968e15b45..386a081f5c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5430,14 +5430,14 @@ assessment, principal component analysis on codon coverage.") (define-public r-riboseqr (package (name "r-riboseqr") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "riboSeqR" version)) (sha256 (base32 - "1m5w2j35wr0lzwir4s58z757vrcsj5mglsqrkvs241k0hlmn06qa")))) + "0nnhjvjl4c9yyfzjf8kcj4yky5cdimicp7lz008sczy19jq4vjhd")))) (properties `((upstream-name . "riboSeqR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 3dac6963f93b63ebcc657a88b713af034d94587e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:13 +0000 Subject: gnu: r-interactionset: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-interactionset): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 386a081f5c..d0d72f6ad9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5458,14 +5458,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.") (define-public r-interactionset (package (name "r-interactionset") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 - "034xidjmn67n1471fnpdmz7gjm6p05cj8sp9nssc3gxdzn54a6xb")))) + "19m2mpby73zanai68rlqvzx9zccli4dz4kix93acrw9755xp3bsw")))) (properties `((upstream-name . "InteractionSet"))) (build-system r-build-system) -- cgit 1.4.1 From 6371513fd0011c3bdbd13fecdaf97bc8c0cbb091 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:14 +0000 Subject: gnu: r-genomicinteractions: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-genomicinteractions): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d0d72f6ad9..fc079b2b91 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5492,14 +5492,14 @@ experiments.") (define-public r-genomicinteractions (package (name "r-genomicinteractions") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicInteractions" version)) (sha256 (base32 - "0zjl7rp5fk14kqsx0bkbpq6hqahbkiyvwa9aggp4kfb8hnmz9qal")))) + "090kxq5jn1jfr9fgbkvbjr5g4bcxzgsaal3gc9yx1n7pgmhccfmb")))) (properties `((upstream-name . "GenomicInteractions"))) (build-system r-build-system) -- cgit 1.4.1 From e9feedb9024dbc9e08b34723262467969469d712 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:14 +0000 Subject: gnu: r-ctc: Update to 1.68.0. * gnu/packages/bioconductor.scm (r-ctc): Update to 1.68.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fc079b2b91..7ff337f4ee 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5533,14 +5533,14 @@ information and producing various plots and statistics.") (define-public r-ctc (package (name "r-ctc") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ctc" version)) (sha256 (base32 - "1v8aysvy6a3r1iafc3xvk885c128kb3pb9zpcdhdjcn0by96k8hh")))) + "1yq5igwzcwfhxy49qf3pralpikiqq7sqr1cig8mkpjpaj5bbaayx")))) (build-system r-build-system) (propagated-inputs `(("r-amap" ,r-amap))) (home-page "https://bioconductor.org/packages/ctc/") -- cgit 1.4.1 From 6ad43d2d7814314b4e140d89deab929f971e14f2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:14 +0000 Subject: gnu: r-goseq: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-goseq): Update to 1.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7ff337f4ee..7eb2cee36b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5553,14 +5553,14 @@ trees and clusters to other programs.") (define-public r-goseq (package (name "r-goseq") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "goseq" version)) (sha256 (base32 - "07qrxssx4rb8r958r1smx8xfpzdxpp55hci3201hcmz3mxz77i0s")))) + "1psl9mqgx1d21kayaxvrxriw34fq30wnd57q5c1sk3p8iahg73g0")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit 1.4.1 From 9050a5c7f657ccf350469180b11b04b2a9ec1310 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:14 +0000 Subject: gnu: r-glimma: Update to 2.4.0. * gnu/packages/bioconductor.scm (r-glimma): Update to 2.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7eb2cee36b..6dcefe6296 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5579,14 +5579,14 @@ defined categories which are over/under represented in RNA-seq data.") (define-public r-glimma (package (name "r-glimma") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Glimma" version)) (sha256 (base32 - "0dsk8qmwimzmd1x4k4jwg9q11jm1ahn8cw0gzd6s2gmigfls4hsa")))) + "0qkbx9n2vb7kvb5f00csnbffy5bm7hhbdvkx2isgzi0wv0y59kx9")))) (properties `((upstream-name . "Glimma"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From e5cd10e99df12d859ac1852fadecc9f53d8bd2b8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:14 +0000 Subject: gnu: r-rots: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-rots): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6dcefe6296..d0276a5330 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5612,14 +5612,14 @@ information.") (define-public r-rots (package (name "r-rots") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROTS" version)) (sha256 (base32 - "18wyi73l95df182vg3m014sxwdbpggr61vsbazhyw4vyx2fnzmpl")))) + "0qhy984y83a3nf4zw54rasw3vn932q4zb3gljifkw701jnrzqmki")))) (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 92f690c1b0795cd9f01299798919ad5661d5f886 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:14 +0000 Subject: gnu: r-plgem: Update to 1.66.0. * gnu/packages/bioconductor.scm (r-plgem): Update to 1.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d0276a5330..0b2bd6031e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5636,14 +5636,14 @@ in omics data.") (define-public r-plgem (package (name "r-plgem") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "plgem" version)) (sha256 (base32 - "1rz5jk5bgpk7gjknx79jyslahjg46q2f4bx6dgd0vwmarc29a45z")))) + "06w8xlw4j1fc9ipdgw55dvhp07f04icmhr20lqzwwhqd5pskrra3")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit 1.4.1 From fff0fe2ec91abd05154cc6991b3bccc33f649e6d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:15 +0000 Subject: gnu: r-inspect: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-inspect): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0b2bd6031e..3a4c71b425 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5661,14 +5661,14 @@ genes or proteins in these datasets.") (define-public r-inspect (package (name "r-inspect") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "0jh5db9dv5pb6b50sg22x8q55m3h0h0nkmb9mivvvp22dhyrd82z")))) + "072kv5k3giyll1clzrg0anqhyl4qbi7cjnmkqz25zdl5bab9l7jk")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 6f2ef7761a0bf1e38cfee9164c7a88b631f4aa8e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:15 +0000 Subject: gnu: r-dnabarcodes: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-dnabarcodes): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3a4c71b425..a1a9dc2a34 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5708,14 +5708,14 @@ modeling the rates that determines changes in mature mRNA levels.") (define-public r-dnabarcodes (package (name "r-dnabarcodes") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNABarcodes" version)) (sha256 (base32 - "1wiqmzjcb7flp7ldcgbx91asxxrmm1rg9pcfljniab9xcsldhksp")))) + "07yaz98r18mjny1ilmfnjxcra7xpklnd183pw0kasvsri01ccwxg")))) (properties `((upstream-name . "DNABarcodes"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 7ec0b978de65bac7ba4419161bd96919c7291d67 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:15 +0000 Subject: gnu: r-ruvseq: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-ruvseq): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a1a9dc2a34..39c3bf0e3b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5737,14 +5737,14 @@ demultiplexed, i.e. assigned to their original reference barcode.") (define-public r-ruvseq (package (name "r-ruvseq") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RUVSeq" version)) (sha256 (base32 - "1fy0k1p0m209lzjpd5jhfnifa22lrn63qq3a3kn5g0xhbbmijzac")))) + "1a19klscykdgsd7izcxyr45ml7g0gpdj65gvbaw124mal2p4zi9q")))) (properties `((upstream-name . "RUVSeq"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 651d54ef51855c0c0e89ac777e17ed1ddd37fb4f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:15 +0000 Subject: gnu: r-biocneighbors: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-biocneighbors): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 39c3bf0e3b..c8eb73c1f6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5765,14 +5765,14 @@ samples.") (define-public r-biocneighbors (package (name "r-biocneighbors") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocNeighbors" version)) (sha256 (base32 - "0cjidi18wjip9xzx83890wjk40vvjq06prf1ag4m2kac47w01r7v")))) + "04in8l6j7frgm0a5dzphazfhn9cm8w775z5yir712jxa37mh1agr")))) (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 496260ddf1e8c73c53918f383a2a9ea389e60724 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:15 +0000 Subject: gnu: r-scaledmatrix: Update to 1.2.0. * gnu/packages/bioconductor.scm (r-scaledmatrix): Update to 1.2.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c8eb73c1f6..6fc98ab510 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5797,14 +5797,14 @@ achieved for all methods using the BiocParallel framework.") (define-public r-scaledmatrix (package (name "r-scaledmatrix") - (version "1.0.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ScaledMatrix" version)) (sha256 (base32 - "1j96fvw1waqxbv5c8myfmhsidq370z03yz13yqmrs4nn1rpn1a06")))) + "0vz8441gl5gycy1ypybwhq97bnyvhhlg6gxpi1dsdy2c9b6d81kc")))) (properties `((upstream-name . "ScaledMatrix"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From eb7a7bacbcc601eb4f19a49307f9f0a9bb007956 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:15 +0000 Subject: gnu: r-treeio: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-treeio): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6fc98ab510..18369cc1be 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5825,14 +5825,14 @@ multiplication.") (define-public r-treeio (package (name "r-treeio") - (version "1.16.2") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "treeio" version)) (sha256 (base32 - "1y60yvg1rl21cab9xrkns0209pg44mwr90qj099dvk97wsjkx67g")))) + "03gz378qrp6b9fcriqanfnphibqv4bxhvz48rigzkidkzz71wfaj")))) (properties `((upstream-name . "treeio"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 9a79db434ab03e89017d9b85a8d8c7854023bd8c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:15 +0000 Subject: gnu: r-ggtree: Update to 3.2.0. * gnu/packages/bioconductor.scm (r-ggtree): Update to 3.2.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 18369cc1be..afa12012f6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5857,14 +5857,14 @@ platform for merging tree with associated data and converting file formats.") (define-public r-ggtree (package (name "r-ggtree") - (version "3.0.4") + (version "3.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggtree" version)) (sha256 (base32 - "0xf4b9vfdyzzivwgw4ymapl5bb4k9p04mmr53822kxgfd5qrs1zx")))) + "1c6b7kjh44k096v8mhn53abr181vpbn7s6ab7zk4phnsyfxsclxb")))) (properties `((upstream-name . "ggtree"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From fae42c164b1cc4ef55874bf29bc3fec9db7eabcc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:16 +0000 Subject: gnu: r-metapod: Update to 1.2.0. * gnu/packages/bioconductor.scm (r-metapod): Update to 1.2.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index afa12012f6..ebb1f979e6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5894,14 +5894,14 @@ data.") (define-public r-metapod (package (name "r-metapod") - (version "1.0.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "metapod" version)) (sha256 (base32 - "1hbcwr6d8gyrf4azh0gi588xkrg6gz7gsb5hbvzqkhplbsp6shlv")))) + "1s8dfzpgbpxbn3jvx891gvw3jyn43nlxb73yv1vjn85brk9zbqpk")))) (properties `((upstream-name . "metapod"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 8c6a0221fbeedccdb319c5e0b3050850fcc24ba1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:16 +0000 Subject: gnu: r-biocsingular: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-biocsingular): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ebb1f979e6..4418a827c3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5923,14 +5923,14 @@ missing values and weighting where appropriate.") (define-public r-biocsingular (package (name "r-biocsingular") - (version "1.8.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSingular" version)) (sha256 (base32 - "16gkwq8fb8jdchpnlzq2hz3i74a6pzbnc1bf93282h11mp7qr58l")))) + "0dkh6a23qymjcynppmpp3k1mzpfadv8dqyz410pxkqsxig4ldd4n")))) (properties `((upstream-name . "BiocSingular"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 5c53d2145051f89300928c926b6d635a09c05ca1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:16 +0000 Subject: gnu: r-savr: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-savr): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4418a827c3..e38f68a822 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6002,14 +6002,14 @@ maps.") (define-public r-savr (package (name "r-savr") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "savR" version)) (sha256 (base32 - "1ynp334hm76zf05j4f6vha6r16s5f2ncxx9yviq4rxidk9r723jq")))) + "0dwl94j5dm5ngn8lyyc4bd9ihd1nqincvq26najjn6lw0x55ciky")))) (properties `((upstream-name . "savR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 7c4992115c64a317f0b2ca945b4520c50a2be5fd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:16 +0000 Subject: gnu: r-chipexoqual: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-chipexoqual): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e38f68a822..7111763f2b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6028,14 +6028,14 @@ Viewer (SAV) files, access data, and generate QC plots.") (define-public r-chipexoqual (package (name "r-chipexoqual") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPexoQual" version)) (sha256 (base32 - "0fbrf5s6pz115djm7xw95k1d0p7svi40aacbb3d52wmx5azwj424")))) + "1hh3mhfcngyx7cpzns8mjqviy8vfzrvxpv6nyizflpfmsr39mxfk")))) (properties `((upstream-name . "ChIPexoQual"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From efb1b28f3253603f905ab006657cff12f3e7435c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:16 +0000 Subject: gnu: r-copynumber: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-copynumber): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7111763f2b..78968f339c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6068,13 +6068,13 @@ sequencing data.") (define-public r-copynumber (package (name "r-copynumber") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "copynumber" version)) (sha256 (base32 - "03pvjzjrcsbjfw3855s3whfzin45vaipy7cahnj6fywdysvh8hps")))) + "143ifvjkjz0392drm82xmpj1f8b5pc2dyyxyc9dkqmay8lf1n534")))) (build-system r-build-system) (propagated-inputs `(("r-s4vectors" ,r-s4vectors) -- cgit 1.4.1 From e639d03112aa499978454cec2188686fe9d93e26 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:16 +0000 Subject: gnu: r-dnacopy: Update to 1.68.0. * gnu/packages/bioconductor.scm (r-dnacopy): Update to 1.68.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 78968f339c..592f8c4b40 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6091,14 +6091,14 @@ penalized least squares regression method.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "0mgq814f6c2271d2lxg763bsnv3ma4ari5xa4x1rbksv8yvcjc4d")))) + "19ax431i97r49gh1232vf8mgmkvc6k26lnq44j3g10n6q01czswm")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) -- cgit 1.4.1 From d9b6a4229747620ce282c0ff3325deaba78d9a51 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:17 +0000 Subject: gnu: r-ebseq: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-ebseq): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 592f8c4b40..9e3ecc8162 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6191,14 +6191,14 @@ and regression inferences from RNA-sequencing data.") (define-public r-ebseq (package (name "r-ebseq") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBSeq" version)) (sha256 (base32 - "0h5v3vrb90zim80bdnr3aw58g3h7zjqa4l9i0jwx5j19ywf54fdz")))) + "1p8i04v5h6mbc8zqbf3rifbwwylzzc1fqrkhh0a0mbcgq2nv7i9m")))) (properties `((upstream-name . "EBSeq"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 2b0a656fd7bd807c3387c3e478d218ee450fa8b6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:17 +0000 Subject: gnu: r-karyoploter: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-karyoploter): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9e3ecc8162..cc6a472186 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6215,13 +6215,13 @@ gene and isoform level using RNA-seq data") (define-public r-karyoploter (package (name "r-karyoploter") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "karyoploteR" version)) (sha256 (base32 - "11sgxz2xz685pgm8mf0hzm6aryx4fj5g3dlffjzpqxh3awfqa19p")))) + "0x3mld9q55r2fy452wxq5sjzmms10zmpkzs71c3w1fdli5hwszdq")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit 1.4.1 From b5e67f574792e03800538b622227669cfeb4238e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:17 +0000 Subject: gnu: r-lpsymphony: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-lpsymphony): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cc6a472186..25427236dd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6253,14 +6253,14 @@ coordinates.") (define-public r-lpsymphony (package (name "r-lpsymphony") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 - "0aw4b3p5z8ys7zlwy8s3bsqk03xwx42311yxr7q14w3f7sn3shzn")))) + "1bv28b1fgcazv6j0xw4nn6wljs37qnkyahqy7anrwissdpryhjfs")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) -- cgit 1.4.1 From 3835d77db37c8c1709e2e44239b30e7010f32214 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:17 +0000 Subject: gnu: r-ihw: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-ihw): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 25427236dd..658f25df54 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6283,14 +6283,14 @@ to install interface to SYMPHONY.") (define-public r-ihw (package (name "r-ihw") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IHW" version)) (sha256 (base32 - "0b393a8ayzbnrgkk562w1dj7avacpb3wc7yq7awiki24wi5g2lfw")))) + "0vgij5zyaw3fh7arkg4jy1mizsqzbkcsjl05mh3ng2bqh30kyqqx")))) (properties `((upstream-name . "IHW"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 25dc8fb984f2c2ab9932ffafa7c361276080cd24 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:17 +0000 Subject: gnu: r-icobra: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-icobra): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 658f25df54..9854190582 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6315,14 +6315,14 @@ independent of the p-value under the null hypothesis.") (define-public r-icobra (package (name "r-icobra") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iCOBRA" version)) (sha256 (base32 - "190rkx3sivj68in36hhin5v535yd6fvlvm7l90w1bl38zpb7p6jn")))) + "0qg32g1rfvh6mx8wny1lrva9vc347288hzml7yb4rnrsx1hggkpa")))) (properties `((upstream-name . "iCOBRA"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 2953aac54a35125ea3c7f360b2655097d915845d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:17 +0000 Subject: gnu: r-residualmatrix: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-residualmatrix): Update to 1.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9854190582..647e99aa08 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6351,14 +6351,14 @@ interactive exploration of results.") (define-public r-residualmatrix (package (name "r-residualmatrix") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ResidualMatrix" version)) (sha256 (base32 - "0p7va19aw0j6anx7ck879kbi5cn7dy712h5ia94adr38ssismv1v")))) + "0xsn4fm34a7xpkgmx3a1j2xzdaxf2hyla1062wqn04kw0k9y29vg")))) (properties `((upstream-name . "ResidualMatrix"))) (build-system r-build-system) -- cgit 1.4.1 From 78018d3c5ced0da187436e0bd78a954482fd6d18 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:18 +0000 Subject: gnu: r-batchelor: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-batchelor): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 647e99aa08..8642880d18 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6382,14 +6382,14 @@ multiplication and calculation of row/column sums or means.") (define-public r-batchelor (package (name "r-batchelor") - (version "1.8.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "batchelor" version)) (sha256 (base32 - "1bkk69b5llkmvmpsnhymwjm2szmzypgszfsw8mak1b5ms5zf8lr0")))) + "0axkic11bwjbw8apwxx6p51s7jvlwhq7xi1bdknn54k86axq84dr")))) (properties `((upstream-name . "batchelor"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From aa5a9e5d6314f9897a38ba5b79399d86c56cf496 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:18 +0000 Subject: gnu: r-mast: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-mast): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8642880d18..1048de7f68 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6425,14 +6425,14 @@ the numbers of cells across batches.") (define-public r-mast (package (name "r-mast") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MAST" version)) (sha256 (base32 - "1gkpagam5rap36viyr3n4psa658x9vckrxap1h67jasiiyrcfz2d")))) + "14h6giny9lhzqjsx3h7gdhsm8wfwnvp5zsl4avrflip0jmsn45yy")))) (properties `((upstream-name . "MAST"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 2b78b19ed831da8321f2d9599cce5eaa23069c97 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:18 +0000 Subject: gnu: r-monocle: Update to 2.22.0. * gnu/packages/bioconductor.scm (r-monocle): Update to 2.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1048de7f68..19142c8c90 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6460,14 +6460,14 @@ single cell assay data.") (define-public r-monocle (package (name "r-monocle") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "monocle" version)) (sha256 (base32 - "05j1vc51f39xalggdq27y7218gkr3zq7fh7jhzsb4jj7fpn837ry")))) + "0wb2c1jf502lrfx3d0amb09fvhalrwxvpsp99jsab162v4hddg85")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit 1.4.1 From b5235660c8783676e006859e39ba87ecae69e719 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:18 +0000 Subject: gnu: r-noiseq: Update to 2.38.0. * gnu/packages/bioconductor.scm (r-noiseq): Update to 2.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 19142c8c90..550187fd64 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6617,14 +6617,14 @@ several functions from the R igraph package.") (define-public r-noiseq (package (name "r-noiseq") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "NOISeq" version)) (sha256 (base32 - "18d51dv2ygsm7kkwal341f1wrwrazyns0045j00vld367kic8jiz")))) + "0mmvzf8y4gm84hgjdpf86b1y37237wp5mc3x1g6sdiz9qi8l356v")))) (properties `((upstream-name . "NOISeq"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From d06be34abdb247dc60aca8681bbf226c29d34869 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:18 +0000 Subject: gnu: r-scdd: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-scdd): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 550187fd64..fb625b4d26 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6644,14 +6644,14 @@ assumptions.") (define-public r-scdd (package (name "r-scdd") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDD" version)) (sha256 (base32 - "1dw9m3m99apmbs32461c6lnmy81n5hxbhz3p8jk419gajkh4v1ji")))) + "0gjdjkpkm9zc9hzzb6r2mknl4zyg7s2lgqppmzzhgcnvlmgvm5b5")))) (properties `((upstream-name . "scDD"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From cf5a3022c9cf6df06e98b1e5ecb638dcfc404c5d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:18 +0000 Subject: gnu: r-scone: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-scone): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fb625b4d26..a363564110 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6682,14 +6682,14 @@ distributions.") (define-public r-scone (package (name "r-scone") - (version "1.16.1") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scone" version)) (sha256 (base32 - "0zw8g4mql7b02xqwhc1i0bnhm20c1q9xqc7yz84j98pqbi996vi5")))) + "1fqlwg195rzpwh35cj941vhmj2plzpn253skig6glr0z2sirr9r1")))) (build-system r-build-system) (propagated-inputs `(("r-aroma-light" ,r-aroma-light) -- cgit 1.4.1 From c14e90b2e06e56ce4c7ef6a2aff11e5978a534fc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:18 +0000 Subject: gnu: r-geoquery: Update to 2.62.0. * gnu/packages/bioconductor.scm (r-geoquery): Update to 2.62.0. [propagated-inputs]: Add r-data-table. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a363564110..3fb4c43c07 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6726,18 +6726,19 @@ high-throughput analyses.") (define-public r-geoquery (package (name "r-geoquery") - (version "2.60.0") + (version "2.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GEOquery" version)) (sha256 (base32 - "0jhkdbcd03d5n8vn3xkad6f21xjkawyxc9rdwcj8vwc8alx730am")))) + "0fkx4jh1s76l015vwikkryarlx6iihb1z935nzpdhah3rpqx3b3z")))) (properties `((upstream-name . "GEOquery"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) + ("r-data-table" ,r-data-table) ("r-dplyr" ,r-dplyr) ("r-httr" ,r-httr) ("r-limma" ,r-limma) -- cgit 1.4.1 From dc7a2b3b96d5d6c0cac1e86bb7a7616009a5b6b8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:19 +0000 Subject: gnu: r-illuminaio: Update to 0.36.0. * gnu/packages/bioconductor.scm (r-illuminaio): Update to 0.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3fb4c43c07..8623edcc04 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6760,14 +6760,14 @@ the bridge between GEO and BioConductor.") (define-public r-illuminaio (package (name "r-illuminaio") - (version "0.34.0") + (version "0.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "illuminaio" version)) (sha256 (base32 - "1sy0i3nbzsw4ymdxaiwpyx1vcg9yp3i8xfjcymqwhv95j3kyglv9")))) + "0icsp610am5vrd8x2h9c450phn4vl9c5wnzqmkix5hkqzrykk34m")))) (build-system r-build-system) (propagated-inputs `(("r-base64" ,r-base64))) -- cgit 1.4.1 From 328050f08398312813ef429ff201731877424450 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:19 +0000 Subject: gnu: r-siggenes: Update to 1.68.0. * gnu/packages/bioconductor.scm (r-siggenes): Update to 1.68.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8623edcc04..33e3fbb8af 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6781,14 +6781,14 @@ files, including IDAT.") (define-public r-siggenes (package (name "r-siggenes") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "siggenes" version)) (sha256 (base32 - "0lva0f255fcpy625frvij4n14q7nw4jcx8n2hlkxid4mgkfqwlhf")))) + "1fymp5ci1nwkk5yfj7hli464xqvvlvzf2a5j0w3qkxly9hrymix9")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit 1.4.1 From 56f8449df1cec24e8550918a6b651c446332234e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:19 +0000 Subject: gnu: r-bumphunter: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-bumphunter): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 33e3fbb8af..f96b0a29cf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6807,14 +6807,14 @@ Bayes Analyses of Microarrays} (EBAM).") (define-public r-bumphunter (package (name "r-bumphunter") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bumphunter" version)) (sha256 (base32 - "0wi38vwfi8qr10x4xifhylxx7vfc6fqvqs649iq7lf0y7islwq2v")))) + "0d5cz9xy7vhcaj5n3h4cfiv08sn7wn83458525pdwvdzzm449xgv")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit 1.4.1 From 74ea385c8aa657e2d6c77047dba1a47237aeae1c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:19 +0000 Subject: gnu: r-minfi: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-minfi): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f96b0a29cf..5ff2daf23f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6841,14 +6841,14 @@ studies.") (define-public r-minfi (package (name "r-minfi") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minfi" version)) (sha256 (base32 - "189lzppvrz6bw2kpppawgsfjyh2ahyy8bi9z8srpas67qf2r8jmj")))) + "0d5220nknwgi1020vhvf7408n5p80dmad66n85af5776qn84a6nx")))) (build-system r-build-system) (propagated-inputs `(("r-beanplot" ,r-beanplot) -- cgit 1.4.1 From d9c9ec4396bf1f7eec6d43c2c3ce3119363f087a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:19 +0000 Subject: gnu: r-methylumi: Update to 2.40.1. * gnu/packages/bioconductor.scm (r-methylumi): Update to 2.40.1. [propagated-inputs]: Add r-genomicfeatures. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5ff2daf23f..40509e10ba 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6892,14 +6892,14 @@ methylation arrays.") (define-public r-methylumi (package (name "r-methylumi") - (version "2.38.0") + (version "2.40.1") (source (origin (method url-fetch) (uri (bioconductor-uri "methylumi" version)) (sha256 (base32 - "1941rc524ssx8gwhmwk40mgfrhddfs6hgldvs7bi22r29gm4y7qj")))) + "1lfcsv8k9c4ndfwlbdk3vd7fq58100bfijyxklna41zf8m8kkkka")))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) @@ -6909,6 +6909,7 @@ methylation arrays.") ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19) ("r-genefilter" ,r-genefilter) ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-illuminaio" ,r-illuminaio) -- cgit 1.4.1 From f151723cb6768a2b50a9b20c94351f345a0bcc18 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:19 +0000 Subject: gnu: r-lumi: Update to 2.46.0. * gnu/packages/bioconductor.scm (r-lumi): Update to 2.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 40509e10ba..c5ba21db1c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6939,14 +6939,14 @@ and Infinium HD arrays are also included.") (define-public r-lumi (package (name "r-lumi") - (version "2.44.0") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lumi" version)) (sha256 (base32 - "0qjdxjdzfnnxcm07bf51v38388s5qf1i03l1sdb9jf3gxdh8yh02")))) + "0v33p66vn4alhx2il9wwdvc9sqvgasgj0s2gk85gjc76ad0017in")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) -- cgit 1.4.1 From 327371f61ff37f60d988fa6578bb2d66ba342a38 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:20 +0000 Subject: gnu: r-linnorm: Update to 2.18.0. * gnu/packages/bioconductor.scm (r-linnorm): Update to 2.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c5ba21db1c..12ada36618 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6978,14 +6978,14 @@ especially Illumina Infinium methylation microarrays.") (define-public r-linnorm (package (name "r-linnorm") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 - "035hrniycqadmkwg8rmzw8szv0amhy31390izy91rfrld31v2yy7")))) + "1bdnglznsfs1kdscqyjv595wiy09khcv9kxm4fmbnmksisqjz5qj")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 06c89769c68e3002c182b9d2ce4f53d6f6826973 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:20 +0000 Subject: gnu: r-ioniser: Update to 2.18.0. * gnu/packages/bioconductor.scm (r-ioniser): Update to 2.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 12ada36618..ea34aaceba 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7039,14 +7039,14 @@ evaluation of DEG analysis methods.") (define-public r-ioniser (package (name "r-ioniser") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IONiseR" version)) (sha256 (base32 - "0fknlwdfd49v09zspg0337b0zzc8hqza3563yrw51viw3g35d6q3")))) + "1hdg446z5s616aaalzz49if1wp9nmzm2mbyva82m1vz8i7ih9m4h")))) (properties `((upstream-name . "IONiseR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 07e49dac6fcd4dc902624227efcd69b1abb5562f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:20 +0000 Subject: gnu: r-tradeseq: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-tradeseq): Update to 1.8.0. [propagated-inputs]: Remove r-monocle; add r-mass and r-trajectoryutils. --- gnu/packages/bioconductor.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ea34aaceba..fff492067f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7136,13 +7136,13 @@ published results; and a routine for graphical display.") (define-public r-tradeseq (package (name "r-tradeseq") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tradeSeq" version)) (sha256 (base32 - "0fgmb309pvqf3chdhqgbd4lzhahcj5g71sica33nzn98qhipldx7")))) + "1s5anbb38gi5sfkxy19zpvkj8d0ij7m6cd0z4gmx4f5pf7pz0m3j")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -7151,10 +7151,10 @@ published results; and a routine for graphical display.") ("r-ggplot2" ,r-ggplot2) ("r-igraph" ,r-igraph) ("r-magrittr" ,r-magrittr) + ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) ("r-matrixstats" ,r-matrixstats) ("r-mgcv" ,r-mgcv) - ("r-monocle" ,r-monocle) ("r-pbapply" ,r-pbapply) ("r-princurve" ,r-princurve) ("r-rcolorbrewer" ,r-rcolorbrewer) @@ -7163,6 +7163,7 @@ published results; and a routine for graphical display.") ("r-slingshot" ,r-slingshot) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-tibble" ,r-tibble) + ("r-trajectoryutils" ,r-trajectoryutils) ("r-viridis" ,r-viridis))) (native-inputs `(("r-knitr" ,r-knitr))) -- cgit 1.4.1 From a2b346ab138867aa0fe24952026dfe7e1146b6e6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:20 +0000 Subject: gnu: r-varianttools: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-varianttools): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fff492067f..8a43f558dd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7207,14 +7207,14 @@ peak definition in combination with known profile characteristics.") (define-public r-varianttools (package (name "r-varianttools") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantTools" version)) (sha256 (base32 - "1gpzrln2clfrja8rzxhsis6bi1xqglh3h2lhvqlnrx4lqxhbkv9c")))) + "0079dsgav4q03c4i0dhggc88iifd828n73kjv3sahim9akafdshl")))) (properties `((upstream-name . "VariantTools"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 75f1085c2f1f185b2b3c29d22bcfb0bbde9b43b7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:20 +0000 Subject: gnu: r-heatplus: Update to 3.2.0. * gnu/packages/bioconductor.scm (r-heatplus): Update to 3.2.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8a43f558dd..734c9ea6a1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7247,14 +7247,14 @@ gmapR.") (define-public r-heatplus (package (name "r-heatplus") - (version "3.0.0") + (version "3.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Heatplus" version)) (sha256 (base32 - "0xwg3sxmihg3p6v3nxgrqy0nrqxi6razg3b3rjh2gcb2vv8gcqng")))) + "0yrnjrbfn8vjzvp2742lyxdqca4s18h73j44qxw7ib95x3p4lndf")))) (properties `((upstream-name . "Heatplus"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 46c97a358fbd088dc2aa0aa1c7423b0474c1db64 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:20 +0000 Subject: gnu: r-gosemsim: Update to 2.20.0. * gnu/packages/bioconductor.scm (r-gosemsim): Update to 2.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 734c9ea6a1..de54c57ff0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7272,14 +7272,14 @@ information about samples and features can be added to the plot.") (define-public r-gosemsim (package (name "r-gosemsim") - (version "2.18.1") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 - "00dbgkiv9x7g2i0anzcxpycwqqqry0y7jl3ad93lhvi31qnqq1sm")))) + "15qi69kkgah7g25bymk9q1xf16hp1rd040fglg0svnydylg2d0ab")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From bc406e02bb6253b55ffc01964c518211220d0a5c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:21 +0000 Subject: gnu: r-anota: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-anota): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index de54c57ff0..43e8d25593 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7301,14 +7301,14 @@ sets of GO terms, gene products and gene clusters.") (define-public r-anota (package (name "r-anota") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "anota" version)) (sha256 (base32 - "039bmcv5l44gszb6xapbihp3mfqdaaa8mfc05y702p78i7x93g5y")))) + "0agvcpb3lr9v55h53ywf662gpxayivxacv8dcm526cc8i8hdqa9f")))) (build-system r-build-system) (propagated-inputs `(("r-multtest" ,r-multtest) -- cgit 1.4.1 From 7ac356d3374a7bce933319c13465dd580e9742dc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:21 +0000 Subject: gnu: r-sigpathway: Update to 1.62.0. * gnu/packages/bioconductor.scm (r-sigpathway): Update to 1.62.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 43e8d25593..2509a8ede5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7332,14 +7332,14 @@ the data set is suitable for such analysis.") (define-public r-sigpathway (package (name "r-sigpathway") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sigPathway" version)) (sha256 (base32 - "1xz5nbw5dzyah8az7mpwj8m27fsvpi2jjhfg3n27dsv8rvdncqi8")))) + "1c46m1gbgiygcj8m65h8iwzk3fkp6nynd6rk1f5qdh7kw5ap28f9")))) (properties `((upstream-name . "sigPathway"))) (build-system r-build-system) (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") -- cgit 1.4.1 From bca9a6b4c1ae9247ecf39ba5150b12a1d4bb0b9f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:21 +0000 Subject: gnu: r-fcscan: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-fcscan): Update to 1.8.0. [propagated-inputs]: Add r-doparallel and r-foreach. --- gnu/packages/bioconductor.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2509a8ede5..184d84c339 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7354,17 +7354,19 @@ phenotype of interest.") (define-public r-fcscan (package (name "r-fcscan") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fcScan" version)) (sha256 - (base32 "10fcz741dr3wbb9f63qywlrays4cnvfnsm6yw4bmkrwk6ccijg8h")))) + (base32 "0b161ayq4m9xxfs0lgw632lgygzabz8gjl0n75050pa7qaazknvd")))) (properties `((upstream-name . "fcScan"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicranges" ,r-genomicranges) + `(("r-doparallel" ,r-doparallel) + ("r-foreach" ,r-foreach) + ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-plyr" ,r-plyr) ("r-rtracklayer" ,r-rtracklayer) -- cgit 1.4.1 From 6dbc856518c38d1c01ae54f32a2a9afd666faba4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:21 +0000 Subject: gnu: r-fgsea: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-fgsea): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 184d84c339..fe4c42a79c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7387,14 +7387,14 @@ presence of additional sites within the allowed window size.") (define-public r-fgsea (package (name "r-fgsea") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fgsea" version)) (sha256 (base32 - "1mhdgy46nxgv7v54bk9bqfy0vgjzl1law7zy718swdd762xn6g9d")))) + "10flcdm4b1kxnsvhl4k6mwkzb1vbai33k291j8nsrhj2cl5l8gm9")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) -- cgit 1.4.1 From 9b6dee4c0d45d59ce0f74c15811e3cfc6d411d4f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:21 +0000 Subject: gnu: r-dose: Update to 3.20.0. * gnu/packages/bioconductor.scm (r-dose): Update to 3.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fe4c42a79c..503eb5e33d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7419,14 +7419,14 @@ to multiple hypothesis correction.") (define-public r-dose (package (name "r-dose") - (version "3.18.3") + (version "3.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "09blmrgzxaknn263zf3zqc5yx27wjwznsr8lqsm118k4wpfxj504")))) + "0hj5hn54g8a3gj4q9200bffcy9m1mvkiwbg60ysv1hxxbpi57kmv")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 498f45bcad1e9363e024ff5de79a94543a238290 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:22 +0000 Subject: gnu: r-enrichplot: Update to 1.14.1. * gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.14.1. [propagated-inputs]: Remove r-cowplot; add r-aplot and r-yulab-utils. --- gnu/packages/bioconductor.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 503eb5e33d..4a7052f8e5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7454,17 +7454,17 @@ data.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.12.3") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "0a4v7ymy9jn66iw093jngzszkvr2mfzzlxp0h6nnvlbnbvqqzgm3")))) + "0nsx96mkcg0hhg3x8jndzq3xvq9bq7m4yf1b3ry73b17ladx81ch")))) (build-system r-build-system) (propagated-inputs - `(("r-cowplot" ,r-cowplot) + `(("r-aplot" ,r-aplot) ("r-dose" ,r-dose) ("r-ggplot2" ,r-ggplot2) ("r-ggraph" ,r-ggraph) @@ -7477,7 +7477,8 @@ data.") ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-reshape2" ,r-reshape2) ("r-scatterpie" ,r-scatterpie) - ("r-shadowtext" ,r-shadowtext))) + ("r-shadowtext" ,r-shadowtext) + ("r-yulab-utils" ,r-yulab-utils))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/GuangchuangYu/enrichplot") -- cgit 1.4.1 From 2e9821cd11bfe63aee1a9ed625ad794eaa75e6f6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:22 +0000 Subject: gnu: r-clusterprofiler: Update to 4.2.0. * gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.2.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4a7052f8e5..f16b6aaf7a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7492,14 +7492,14 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "4.0.5") + (version "4.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "1dccrl2ffhgmv3iqlmpln7z86ahpf0j9ma194fnknsgi3cd9rhrl")))) + "18y7482sw0awlhazikq13r2r0zid9ksk942rma87m448y1cq2fi5")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) -- cgit 1.4.1 From b4127b3490c1707d18c7fcfff38886879ee8ecc0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:22 +0000 Subject: gnu: r-clusterexperiment: Update to 2.14.0. * gnu/packages/bioconductor.scm (r-clusterexperiment): Update to 2.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f16b6aaf7a..9f8a36df72 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7529,13 +7529,13 @@ profiles (GO and KEGG) of gene and gene clusters.") (define-public r-clusterexperiment (package (name "r-clusterexperiment") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterExperiment" version)) (sha256 (base32 - "1fhmayciwn1m124b4dcs3gzbghgk9f7a7qmjnvvxc958cywcwkx5")))) + "0riray1f841d5fx6mbcki5xmqz21kg5q5l0qz4pkgg9c1d9f7mbc")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) -- cgit 1.4.1 From 58c2b7978f8e831894004307edd90c2f14b357cc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:22 +0000 Subject: gnu: r-mlinterfaces: Update to 1.74.0. * gnu/packages/bioconductor.scm (r-mlinterfaces): Update to 1.74.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9f8a36df72..24f7d921b5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7575,14 +7575,14 @@ expression data sets.") (define-public r-mlinterfaces (package (name "r-mlinterfaces") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MLInterfaces" version)) (sha256 (base32 - "0ipzv7wdvfqhdyjiak956qq201igsdxm6dr6rh3dj6cssgsrnrpb")))) + "1nzy04fqwzb0ywiafgx3m3i2n1b0g4pcg8mlgh8yz5d3mmna4kag")))) (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 85c2a802f917438f75e0229f70ea4e7533fb6d26 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:22 +0000 Subject: gnu: r-annaffy: Update to 1.66.0. * gnu/packages/bioconductor.scm (r-annaffy): Update to 1.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 24f7d921b5..ef80c6c1c4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7617,14 +7617,14 @@ data in R and Bioconductor containers.") (define-public r-annaffy (package (name "r-annaffy") - (version "1.64.2") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annaffy" version)) (sha256 (base32 - "03y633vgxprd2abhanj4sanmb4ymz7az5aiasxn6wjzawiqjdcb1")))) + "0crj37v571005brdd0ypfx2a7d1f829xxj2hahp2gy8aj9xm4s8l")))) (build-system r-build-system) (arguments `(#:phases -- cgit 1.4.1 From 5785c45e01b4f8be046e9e5115edd273be5681f8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:22 +0000 Subject: gnu: r-a4core: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-a4core): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ef80c6c1c4..00f4f23a12 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7653,14 +7653,14 @@ It allows searching of biological metadata using various criteria.") (define-public r-a4core (package (name "r-a4core") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Core" version)) (sha256 (base32 - "00fi753nsayv0xspavw8r9ni1sim8ng33hp3d3kj2b8ihygd1s10")))) + "074aa52y6c70417lxwrclk613gbs7zv3326g9ndbbzzs5pmnh1y0")))) (properties `((upstream-name . "a4Core"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From c179aae47e352048dc0be292ebf4b054b5f146bd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:23 +0000 Subject: gnu: r-a4classif: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-a4classif): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 00f4f23a12..d076365169 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7678,14 +7678,14 @@ arrays.") (define-public r-a4classif (package (name "r-a4classif") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Classif" version)) (sha256 (base32 - "1lz85bys5dp5d1ir9c9c4wy85wkk62s14niyzzxaqrxpsji2p2iw")))) + "0q50d41n7drj5c9x6njyvzr6bj7glmkp1vpyz6cpj97j2v9nikwb")))) (properties `((upstream-name . "a4Classif"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 0b06e8ee13d2e4eccde18f8de862d7c077d99cf6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:23 +0000 Subject: gnu: r-a4preproc: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-a4preproc): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d076365169..3879776c3f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7708,14 +7708,14 @@ Affymetrix arrays.") (define-public r-a4preproc (package (name "r-a4preproc") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Preproc" version)) (sha256 (base32 - "1jibm2f5glzsrvl64hxc5sf59d4w6ry0f663p619hfr44mi1mpri")))) + "1qzr54w1qys1ppd71i5b57503dijfnnbn516a2mfk5l9l7wr728d")))) (properties `((upstream-name . "a4Preproc"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 9b249fc8a9ba5ecfc8b71ca2c669659c613608e0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:23 +0000 Subject: gnu: r-a4reporting: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-a4reporting): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3879776c3f..a4a0eb4950 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7733,14 +7733,14 @@ is used for preprocessing the arrays.") (define-public r-a4reporting (package (name "r-a4reporting") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Reporting" version)) (sha256 (base32 - "09jjfby5znmg2fdkhpbinx2v21zrfa44qq7cylcn9ipffqx3pk86")))) + "1vyah71gm4ngsgy0y10cdxa9b1g810gqa5pbvb3krh5i6h35smwr")))) (properties `((upstream-name . "a4Reporting"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From c0207d4f7ce90f9c907bc8c96f40bc7c5058042e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:23 +0000 Subject: gnu: r-a4base: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-a4base): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a4a0eb4950..9512462ac8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7757,14 +7757,14 @@ provides reporting features.") (define-public r-a4base (package (name "r-a4base") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Base" version)) (sha256 (base32 - "101w4i0w8n7qhki22qr8l8wk8w6zalzmcywqm2g4238qv7xbnr8p")))) + "0rddxnflvbc6z4sj2h8js8yfh0zhrrwj8fk00wicaqp4rkr5yaxy")))) (properties `((upstream-name . "a4Base"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 172cddcbecceb331573b7b39c73ea3cfd864e3ee Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:23 +0000 Subject: gnu: r-a4: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-a4): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9512462ac8..65f43477e4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7788,14 +7788,14 @@ Affymetrix arrays.") (define-public r-a4 (package (name "r-a4") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4" version)) (sha256 (base32 - "0bwn185admy5k99fkd2dhhvy7x1f75r0mqn5k24dbbg0paw6nnr8")))) + "0mkgim93441zxhn4wmbin9ydl94srsawis0xwx479l0byj88n07m")))) (build-system r-build-system) (propagated-inputs `(("r-a4base" ,r-a4base) -- cgit 1.4.1 From 6b27532feaf0bbde6d6481beb766a1824e30b2b2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:23 +0000 Subject: gnu: r-abseqr: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-abseqr): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 65f43477e4..ccf5651742 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7813,14 +7813,14 @@ Affymetrix arrays.") (define-public r-abseqr (package (name "r-abseqr") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "abseqR" version)) (sha256 (base32 - "1xvk84gd1lfq1icrfwwd6y79zywrisfnc3knprigzzax31aks32c")))) + "1v9g71x689ly107c0qmc5iv8qk63nn6lp7yd03jf7hlcafmvqsvz")))) (properties `((upstream-name . "abseqR"))) (build-system r-build-system) (inputs -- cgit 1.4.1 From 4f6f03fd6e3df3534cb644f809048a35c9c79dd0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:24 +0000 Subject: gnu: r-bacon: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-bacon): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ccf5651742..803e735dde 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7861,14 +7861,14 @@ further downstream analysis on its output.") (define-public r-bacon (package (name "r-bacon") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bacon" version)) (sha256 (base32 - "1yp0675n1g8rxdjdd7w8al5c9jq96h0kfm8218mc50z0p2fasgbj")))) + "13dhma34j9ggryainn4x6qvd3hphpxks5gf0mysia00r9hhpwwlc")))) (build-system r-build-system) (propagated-inputs `(("r-biocparallel" ,r-biocparallel) -- cgit 1.4.1 From 38ca6643c4e556e913ec0d4287be8eef2aa722e9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:24 +0000 Subject: gnu: r-rgadem: Update to 2.42.0. * gnu/packages/bioconductor.scm (r-rgadem): Update to 2.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 803e735dde..e2aef73df7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7888,14 +7888,14 @@ fitting a three-component normal mixture on z-scores.") (define-public r-rgadem (package (name "r-rgadem") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGADEM" version)) (sha256 (base32 - "05drbhjqn5kik6k4h03vr3d2b6pv5rm65lsnkyx4caxxcdii4jzm")))) + "1v8xgqqv7m2kyc38x9ppwsv87ivll5ppd6z76zcxj5yspkkrqw3v")))) (properties `((upstream-name . "rGADEM"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From a906e93378b0bd92f9d29befcd4573f52af09f33 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:24 +0000 Subject: gnu: r-motifdb: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-motifdb): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e2aef73df7..96b30dab8f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7946,12 +7946,12 @@ distributions, modules and filter motifs.") (define-public r-motifdb (package (name "r-motifdb") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MotifDb" version)) (sha256 - (base32 "04cmgg5mw1cqbg95zyfc2imykmdxyff16w26rq97xghcxwiq2b3z")))) + (base32 "0a2zg26zzk7bj5c33mbwl8dx9lh1hns8q8kwp09rbfjdichv7425")))) (properties `((upstream-name . "MotifDb"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 9a27f82d0344226e2256cf420fcc9e5de516ddd8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:24 +0000 Subject: gnu: r-motifbreakr: Update to 2.8.0. * gnu/packages/bioconductor.scm (r-motifbreakr): Update to 2.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 96b30dab8f..f8d148209c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7973,12 +7973,12 @@ frequency matrices from nine public sources, for multiple organisms.") (define-public r-motifbreakr (package (name "r-motifbreakr") - (version "2.6.1") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifbreakR" version)) (sha256 - (base32 "1n6v8a7c27aswmbrlcwcpghf27aplkc6nn923imglc3c0sh2lkrz")))) + (base32 "0lrgy64sv2ma6kylp4lsbwkg6ci1kn6qkk0cvzw3m4k3bgia1npj")))) (properties `((upstream-name . "motifbreakR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 0b8b2b63a2f50d5f0a1d35e54b10e79eefbefed6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:24 +0000 Subject: gnu: r-motifstack: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-motifstack): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f8d148209c..eec12291c1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8024,14 +8024,14 @@ Bioconductor.") (define-public r-motifstack (package (name "r-motifstack") - (version "1.36.1") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifStack" version)) (sha256 (base32 - "140xclzgn5z64v5nm4kvj0qwvqb7ix91bbmimsfc6k1p0l8lwsvv")))) + "1ck6bbnrab8mbf70alfdsrcv6lq0fkvcy3klhcwyxxir7r9sgbaz")))) (properties `((upstream-name . "motifStack"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 2ba1756960d58dfc25555ef79c322d5a54dcffba Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:24 +0000 Subject: gnu: r-genomicscores: Update to 2.6.0. * gnu/packages/bioconductor.scm (r-genomicscores): Update to 2.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index eec12291c1..433f38a1d2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8055,14 +8055,14 @@ type and symbol colors.") (define-public r-genomicscores (package (name "r-genomicscores") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicScores" version)) (sha256 (base32 - "1b8982fj0r7igj749wljsdfn3c985w8n3d5gbhr5rw73llfb8x6w")))) + "18fzi2qi95851ci7qrzwpb7v6fhwp6xi1d1vk11xbygpbvql5mls")))) (properties `((upstream-name . "GenomicScores"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 46de5a7503d1e2f5bbaaa682d0bf231b12b59e30 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:25 +0000 Subject: gnu: r-atacseqqc: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-atacseqqc): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 433f38a1d2..36f16f3b56 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8092,14 +8092,14 @@ position-specific scores within R and Bioconductor.") (define-public r-atacseqqc (package (name "r-atacseqqc") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 - "168g3xkhjzrfjpa1ynifdyfhsxx3rpyrbybsarlzr9kslw1cdkxl")))) + "0i1i3bfkp1xsjdl1nd56mlh66qz3aasd1hp09d4i31njz2f9znwn")))) (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From b7057dbac63a6928f1383d5175d1a4453625d3b1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:25 +0000 Subject: gnu: r-gofuncr: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-gofuncr): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 36f16f3b56..e36e2cbdbc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8139,14 +8139,14 @@ footprints.") (define-public r-gofuncr (package (name "r-gofuncr") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOfuncR" version)) (sha256 (base32 - "0lp2gmjlsk1yqxim5pi26i27iijw11lrcxmji7ynlag359yfnynd")))) + "08n1d03i4l2dl47axmrziiypi83yffndf0ww1b32skyjm2r0x127")))) (properties `((upstream-name . "GOfuncR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From e79f4779ce7805811d84dc1b1f282f71b4502c38 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:25 +0000 Subject: gnu: r-abaenrichment: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-abaenrichment): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e36e2cbdbc..f6db9726a1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8188,14 +8188,14 @@ annotations and ontologies.") (define-public r-abaenrichment (package (name "r-abaenrichment") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABAEnrichment" version)) (sha256 (base32 - "15v5n6d3mnj9d86swkh9agfvrsd065dldaywm1adwmkhhk525wmd")))) + "1sp3f72rzlr822dxx42bswynrwwfx6f520hdhfdikqp13p2y4044")))) (properties `((upstream-name . "ABAEnrichment"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 776c53a967537b04a0365bc56ac438a83c69ba77 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:25 +0000 Subject: gnu: r-annotationtools: Update to 1.68.0. * gnu/packages/bioconductor.scm (r-annotationtools): Update to 1.68.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f6db9726a1..1a89d9c102 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8245,14 +8245,14 @@ different identifieres using the Biocore Data Team data-packages (e.g. (define-public r-annotationtools (package (name "r-annotationtools") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotationTools" version)) (sha256 (base32 - "18dd8saqx17fplvv5sbfz4p9fy7ksy3n9348rd3qlczihcrh9i3w")))) + "0grdswbf8nj0qwl0n5pqsir9242dry85j6m688j81gwwjgmzidvh")))) (properties `((upstream-name . "annotationTools"))) (build-system r-build-system) -- cgit 1.4.1 From 7b6e7ac7bf72aaeb12e1813418236137d14f9538 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:25 +0000 Subject: gnu: r-allelicimbalance: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-allelicimbalance): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1a89d9c102..33f0cd1a9a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8270,14 +8270,14 @@ text files).") (define-public r-allelicimbalance (package (name "r-allelicimbalance") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AllelicImbalance" version)) (sha256 (base32 - "1mn6975npncmfjlpjs3s2pgsrm32xgvnyl2vh1922l6vra97dkrc")))) + "1s6arjd0nxgxyqy7vhqcb78k0ss7vwrhv41pm346hs1nyr5dkzaq")))) (properties `((upstream-name . "AllelicImbalance"))) (build-system r-build-system) -- cgit 1.4.1 From a69776dcb52808445485d1f5ae7a67ba78401b35 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:26 +0000 Subject: gnu: r-aucell: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-aucell): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 33f0cd1a9a..c3066142e7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8313,14 +8313,14 @@ investigation using RNA-seq data.") (define-public r-aucell (package (name "r-aucell") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AUCell" version)) (sha256 (base32 - "0qdac3qalcki20r90k40cc8d0lfywzn9pffg9d719yvs7nrsfdjr")))) + "1lclf8hkhrm6g5fp8yhvjxnwgf8p0j9ffxsmcybz4rjvmwkiz5dp")))) (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 4c18a6b644a8efe9bfdc31b7964438a78df00b77 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:26 +0000 Subject: gnu: r-ebimage: Update to 4.36.0. * gnu/packages/bioconductor.scm (r-ebimage): Update to 4.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c3066142e7..0d6d8bc7e8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8352,14 +8352,14 @@ needed.") (define-public r-ebimage (package (name "r-ebimage") - (version "4.34.0") + (version "4.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBImage" version)) (sha256 (base32 - "1z3cxxg593d66nczz5hh2hdj1d87wc0lxrzc5sn6bp43n351q8h3")))) + "030vpn55ppfqq4408c4db4w40d17x1yq6zajb11p2glikvm1q619")))) (properties `((upstream-name . "EBImage"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 6a4b381268d8f53901675e76b733f18e7d4a739f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:26 +0000 Subject: gnu: r-yamss: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-yamss): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0d6d8bc7e8..3373845bc1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8391,14 +8391,14 @@ visualization with image data.") (define-public r-yamss (package (name "r-yamss") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yamss" version)) (sha256 (base32 - "1al615x778h17jqiyhiyf6djaq9iygs1hlbrna6y4xc0f2kvgxld")))) + "141hbryifm6na5shjyrbjwwksqnl75kqp1m2zl03l9sjqm0kapab")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) -- cgit 1.4.1 From cb48316936a74d14478fca65bfc869e01b86003c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:26 +0000 Subject: gnu: r-gtrellis: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-gtrellis): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3373845bc1..144bc0e1e3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8425,14 +8425,14 @@ analysis.") (define-public r-gtrellis (package (name "r-gtrellis") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gtrellis" version)) (sha256 (base32 - "0l5271cpzjlm4m0v6xcdg2vxlbhn53x1fd59ynb9jwll93av5h1f")))) + "0q2lyb8p1xhqqhw4q1br4r8mwq06mjws8iwbbilkngvs3brbmrzl")))) (build-system r-build-system) (propagated-inputs `(("r-circlize" ,r-circlize) -- cgit 1.4.1 From 2b769d098100658a03c0ac508acd78289383f6b7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:26 +0000 Subject: gnu: r-somaticsignatures: Update to 2.30.0. * gnu/packages/bioconductor.scm (r-somaticsignatures): Update to 2.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 144bc0e1e3..f27e1b79ea 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8454,14 +8454,14 @@ genomic categories and to add self-defined graphics in the plot.") (define-public r-somaticsignatures (package (name "r-somaticsignatures") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SomaticSignatures" version)) (sha256 (base32 - "0jr11c9hz7m49xc8pi6xrr5fhbv68vafvqpzhr0pmm51vvr1vfs9")))) + "1dxzfkvljnydv7kfybfa52dwcbkkci2r8gjspjf90k2bxf10phql")))) (properties `((upstream-name . "SomaticSignatures"))) (build-system r-build-system) -- cgit 1.4.1 From 240e1f0598c7ea359f6a56de719b846b1b4a0dcf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:26 +0000 Subject: gnu: r-yapsa: Update to 1.19.0. * gnu/packages/bioconductor.scm (r-yapsa): Update to 1.19.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f27e1b79ea..6687f088d2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8493,14 +8493,14 @@ decomposition algorithms.") (define-public r-yapsa (package (name "r-yapsa") - (version "1.18.0") + (version "1.19.0") (source (origin (method url-fetch) (uri (bioconductor-uri "YAPSA" version)) (sha256 (base32 - "1xfkgjlm0rxz82qcaqzx95cwirxifd9dsswjg3zcqmz03v7a0gz2")))) + "0fgcbskz96p5815nywsnqv2gzn7g93m438hpd5rpg85srg4wrpdj")))) (properties `((upstream-name . "YAPSA"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 7fc5084e0063bb67d3193330c2894b05900d654a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:26 +0000 Subject: gnu: r-gcrma: Update to 2.66.0. * gnu/packages/bioconductor.scm (r-gcrma): Update to 2.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6687f088d2..db3562bd69 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8542,14 +8542,14 @@ provided.") (define-public r-gcrma (package (name "r-gcrma") - (version "2.64.0") + (version "2.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gcrma" version)) (sha256 (base32 - "1z4abw9s2hs3csnx25nli7fpvb3rh3l0swzl0wfqp087fcs78pxi")))) + "0h7dl4if6skbcqdjdzqyghyswhwpx7xvb54lffz4wdaxpabp3001")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) -- cgit 1.4.1 From 13d51fe643d3c9c93a518bfded7f8498c10cdfa5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:27 +0000 Subject: gnu: r-quantro: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-quantro): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index db3562bd69..7552096ee3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8628,14 +8628,14 @@ chips with the MAQC reference datasets.") (define-public r-quantro (package (name "r-quantro") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "quantro" version)) (sha256 (base32 - "1fkma2ic448h2lrlza8ipg65gpfsz4fhlxcnjpmzhhmzp2xi2p4a")))) + "1r2wbsndc0ji22ap27gbr1wy8icj3cjxwqlz1x0gvxkaj69mwsfq")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit 1.4.1 From b00d8a1e7498441d8516fb357365989dadd0e8da Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:27 +0000 Subject: gnu: r-yarn: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-yarn): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7552096ee3..d32ae9cf10 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8661,14 +8661,14 @@ groups.") (define-public r-yarn (package (name "r-yarn") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yarn" version)) (sha256 (base32 - "1x07l255x52z6cgdc2j8285shqszhr034xm5686rp6d35vah55ji")))) + "0nk4qzrwjiv8q39lgil9x25bm3gpzrnhd37d7754kpxhs2fsmw9d")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit 1.4.1 From 972e9f4224f9d404c5fdee232ee6be9490cede97 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:27 +0000 Subject: gnu: r-roar: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-roar): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d32ae9cf10..4c0cd194fc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8698,14 +8698,14 @@ large RNA-seq experiments.") (define-public r-roar (package (name "r-roar") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "roar" version)) (sha256 (base32 - "0vp0n90rvjm8rzwkbrxa3fasb9val56bz2srz72xwsl3jzb5yk6w")))) + "0hqh4vsnxl2sn1bf6s6wxl2nskb40rhvrysdvb6dr60zkih3g347")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) -- cgit 1.4.1 From 482cec7a53bbd96e2ce173a5b873a85bd74f9954 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:27 +0000 Subject: gnu: r-massspecwavelet: Update to 1.60.0. * gnu/packages/bioconductor.scm (r-massspecwavelet): Update to 1.60.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4c0cd194fc..60a04f2579 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8766,14 +8766,14 @@ genes.") (define-public r-massspecwavelet (package (name "r-massspecwavelet") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MassSpecWavelet" version)) (sha256 (base32 - "1cs32sig1yvqn9xs0cvhfpmkh2lbllx7aab80sz58x03wnx8v60z")))) + "1icqyxkx5a9y3wahkxpxngw85c7l4hih1ym9nwwn9qy93pnw1zi4")))) (properties `((upstream-name . "MassSpecWavelet"))) (build-system r-build-system) -- cgit 1.4.1 From e06acf2682699038d5b83d3a11df08d6d50b8e39 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:27 +0000 Subject: gnu: r-xcms: Update to 3.16.0. * gnu/packages/bioconductor.scm (r-xcms): Update to 3.16.0. [propagated-inputs]: Add r-msfeatures. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 60a04f2579..910d66e798 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8790,14 +8790,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") (define-public r-xcms (package (name "r-xcms") - (version "3.14.1") + (version "3.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "xcms" version)) (sha256 (base32 - "1g8k90p0sbcb3rdrbldj5bcjp2piy5ldni4jplyr78vjpmrmvqk7")))) + "0m6w68ndf2a4k148pbb0bbbgq57akzqgi9nf7k6ngkk22j3m7m95")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -8807,6 +8807,7 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") ("r-lattice" ,r-lattice) ("r-massspecwavelet" ,r-massspecwavelet) ("r-mscoreutils" ,r-mscoreutils) + ("r-msfeatures" ,r-msfeatures) ("r-msnbase" ,r-msnbase) ("r-mzr" ,r-mzr) ("r-plyr" ,r-plyr) -- cgit 1.4.1 From 2704f4d596cb7e3d462bd48e79d34e900969545f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:27 +0000 Subject: gnu: r-wrench: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-wrench): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 910d66e798..eaf18819ab 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8831,14 +8831,14 @@ data for high-throughput, untargeted analyte profiling.") (define-public r-wrench (package (name "r-wrench") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Wrench" version)) (sha256 (base32 - "0yssmqayaryrc0asjjqxdipqdfg309llrzldx38jrfgdsza6bvs0")))) + "1vzv7sswijgb8nq58yrc19wlw2nnpjvans86fqqzs4p8wvq8j06n")))) (properties `((upstream-name . "Wrench"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From a4ab371edf2dea943a5ccc0f3f997b537024fc54 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:28 +0000 Subject: gnu: r-wiggleplotr: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-wiggleplotr): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index eaf18819ab..656aff6b65 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8857,14 +8857,14 @@ that arising from 16s metagenomic surveys.") (define-public r-wiggleplotr (package (name "r-wiggleplotr") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wiggleplotr" version)) (sha256 (base32 - "13f3g6fcc29k0g21mhnypm3nc6qqjw867vamvfkdzynspsfb32ga")))) + "01y1rbmxjza7qx3q33k0r241if69hzkx9plgmj59wyji22lm7syi")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) -- cgit 1.4.1 From b058ff1f753b6cf82be2b82166dfdbfbd1952f2e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:28 +0000 Subject: gnu: r-widgettools: Update to 1.72.0. * gnu/packages/bioconductor.scm (r-widgettools): Update to 1.72.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 656aff6b65..c56943e93b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8891,14 +8891,14 @@ visualization of exonic read coverage.") (define-public r-widgettools (package (name "r-widgettools") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "widgetTools" version)) (sha256 (base32 - "186xgpgyfyi4angxhz6558lfpzvvszzlpyfr8xnbccs3gshk3db2")))) + "0jajfh78116wjfwbmzfvcbxswai4jj9ypzmfhs5j5iypaf8zff8j")))) (properties `((upstream-name . "widgetTools"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/widgetTools/") -- cgit 1.4.1 From d43703c41a7c81c0fb3c78013abf7eea7a4f1b9d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:28 +0000 Subject: gnu: r-webbioc: Update to 1.66.0. * gnu/packages/bioconductor.scm (r-webbioc): Update to 1.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c56943e93b..28a41c69a7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8912,14 +8912,14 @@ widgets in R.") (define-public r-webbioc (package (name "r-webbioc") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "webbioc" version)) (sha256 (base32 - "1mpdw477j78s2nvlf2lzm6mdjcpamyyazjn060h9q3apawn6zajx")))) + "1r3rjvfhqbbzdhlslnc86kr2iip3xgvr81zpvcr8xv9mysgrln17")))) (build-system r-build-system) (inputs `(("netpbm" ,netpbm) -- cgit 1.4.1 From eb5f243f1be71d0b11b8f70ebd113fc4f8d80ffa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:28 +0000 Subject: gnu: r-zinbwave: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-zinbwave): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 28a41c69a7..6c40474189 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8945,14 +8945,14 @@ Currently only Affymetrix oligonucleotide analysis is supported.") (define-public r-zinbwave (package (name "r-zinbwave") - (version "1.14.2") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zinbwave" version)) (sha256 (base32 - "1y8krazz2qdn0wn8ijjs2gn5dl5l960v6bijbkvh0r8066l7viky")))) + "05w95bnq63a339d8x4932k81ycqf825s3qwn98vr52v5g2hv46fq")))) (build-system r-build-system) (propagated-inputs `(("r-biocparallel" ,r-biocparallel) -- cgit 1.4.1 From efbe72addb0bd80c39b641d681e9f8d3619344fc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:28 +0000 Subject: gnu: r-zfpkm: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-zfpkm): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6c40474189..c1b7f0dd57 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8978,14 +8978,14 @@ the data.") (define-public r-zfpkm (package (name "r-zfpkm") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zFPKM" version)) (sha256 (base32 - "1k7xaxr2gn26y8bps5l32g2axfhdn07nbk4q3qcx32d5jm75qkx2")))) + "0fk05vrmyyrhmkwi06lsi553mlpqj3fgwhk1kygz83iqv5z2vfw9")))) (properties `((upstream-name . "zFPKM"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From ba9573b14e67c2fdd9ac4c56daeaa5f3d03b7486 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:28 +0000 Subject: gnu: r-rbowtie2: Update to 2.0.0. * gnu/packages/bioconductor.scm (r-rbowtie2): Update to 2.0.0. [inputs]: Add samtools. [propagated-inputs]: Add r-magrittr and r-rsamtools. --- gnu/packages/bioconductor.scm | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c1b7f0dd57..766e4fab7c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9007,18 +9007,22 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID (define-public r-rbowtie2 (package (name "r-rbowtie2") - (version "1.14.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie2" version)) (sha256 (base32 - "0r5yqjal48xlcv5cidi7p3zwygvsllmv2zzkwkc9kfq083l2i4ih")))) + "0xpvrx2ak9x913sym4l46ycwbnmpcdwb3bf3dfd2gsp0krv8vh1x")))) (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) + (propagated-inputs + `(("r-magrittr" ,r-magrittr) + ("r-rsamtools" ,r-rsamtools))) (inputs - `(("zlib" ,zlib))) + `(("samtools" ,samtools) + ("zlib" ,zlib))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/Rbowtie2/") -- cgit 1.4.1 From 5d77708905ee6667bd0b9b34156caabb67d6fba0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:29 +0000 Subject: gnu: r-progeny: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-progeny): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 766e4fab7c..b69999b562 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9036,14 +9036,14 @@ rapid adapter trimming, identification, and read merging.") (define-public r-progeny (package (name "r-progeny") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "progeny" version)) (sha256 (base32 - "10vpjvl4wps857xiy8rpzr82jzdfbc5rgwh3ir3my26lfws4hfz8")))) + "0zhr5i5v87akzqjb6wid67nhg2icrw6w0awdy87x848c6c1i6j9y")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit 1.4.1 From 2a9f215cd1d4ccb856651df51387f6155ac01eea Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:29 +0000 Subject: gnu: r-arrmnormalization: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-arrmnormalization): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b69999b562..0c94d17618 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9066,14 +9066,14 @@ expression\".") (define-public r-arrmnormalization (package (name "r-arrmnormalization") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ARRmNormalization" version)) (sha256 (base32 - "0ni3vblcadhwxaq1pf1n9jn66cp3bqch68ww4c8zh19zagil2y7r")))) + "1ryqr3mpakjml0jhbk28k2z511sdl87wxdczxq1rwx98s0pc9mnh")))) (properties `((upstream-name . "ARRmNormalization"))) (build-system r-build-system) -- cgit 1.4.1 From f592a0a4ee9d816b63db352268acd3b3cf596589 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:29 +0000 Subject: gnu: r-biocfilecache: Update to 2.2.0. * gnu/packages/bioconductor.scm (r-biocfilecache): Update to 2.2.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0c94d17618..8e538a5dad 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9089,14 +9089,14 @@ Infinium HumanMethylation 450k assay.") (define-public r-biocfilecache (package (name "r-biocfilecache") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocFileCache" version)) (sha256 (base32 - "0ymg4hmabk233qgassld62achjylm12rnidxbakfkx4dvvlbhxxv")))) + "11qayqmgv274hc4h1v222sma07wkxjm8002fl6w3yvi225zq1qc1")))) (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 0e507e00593af5d04d1bd8a8d04092843e0241a4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:29 +0000 Subject: gnu: r-iclusterplus: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-iclusterplus): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8e538a5dad..dfb951fd07 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9122,14 +9122,14 @@ and data files used across sessions.") (define-public r-iclusterplus (package (name "r-iclusterplus") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iClusterPlus" version)) (sha256 (base32 - "1haj25c4cmmjjvh181b41a9pvkh92f7k2w4ljn17iqg31vm45za1")))) + "0w6r2clk8wdnnnjmq3cspmxiq1c8vwprd66xmdrhcqzbjkpkdw2b")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) -- cgit 1.4.1 From 1b455ccb4bf2fd65cfdd0eddcda691153996999e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:29 +0000 Subject: gnu: r-rbowtie: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-rbowtie): Update to 1.34.0. [inputs]: Remove zlib. --- gnu/packages/bioconductor.scm | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dfb951fd07..b701151eab 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9152,18 +9152,16 @@ Gaussian distributions.") (define-public r-rbowtie (package (name "r-rbowtie") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie" version)) (sha256 (base32 - "0mfikbrs28q7r3lnsq0jma5x6nkrnm3q46242jh35w9c969jk5yy")))) + "0ardmryx6ac7v6n900a1klrrldvbmh7bxvy8ldz8rwid19h29ikr")))) (properties `((upstream-name . "Rbowtie"))) (build-system r-build-system) - (inputs - `(("zlib" ,zlib))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/Rbowtie/") -- cgit 1.4.1 From 0187dd1a1d1f42fa777757529957a6b415392f1a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:29 +0000 Subject: gnu: r-sgseq: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-sgseq): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b701151eab..9ea2aa48b3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9175,14 +9175,14 @@ alignment tool.") (define-public r-sgseq (package (name "r-sgseq") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SGSeq" version)) (sha256 (base32 - "0i1yaw8h8gibakvaf1xd6nnjx2bsb2s9c0q74rbq9lm7haihivp6")))) + "15l0r6svs27k82dd472is26shwayz6rs5ylg5gpf3mldr7sa5kja")))) (properties `((upstream-name . "SGSeq"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 80980d827a786fe969719870baf2a8c37e731e12 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:30 +0000 Subject: gnu: r-rhisat2: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-rhisat2): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9ea2aa48b3..76964648f4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9218,14 +9218,14 @@ interpretation.") (define-public r-rhisat2 (package (name "r-rhisat2") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhisat2" version)) (sha256 (base32 - "1hqahh5h22mj2crqp6r9xnm111xmfgk39c100rcaziqrpdy5npk8")))) + "092rws9vjxgm2jpkbp6ign47zmillyyidnc7ylcbn4zr9j5lwv0y")))) (properties `((upstream-name . "Rhisat2"))) (build-system r-build-system) (arguments -- cgit 1.4.1 From e2aa710ca4bcec116b1ba28a11c7537e336833ee Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:30 +0000 Subject: gnu: r-quasr: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-quasr): Update to 1.34.0. [propagated-inputs]: Remove r-biocmanager. --- gnu/packages/bioconductor.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 76964648f4..c4da74cc0b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9258,21 +9258,20 @@ index.") (define-public r-quasr (package (name "r-quasr") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QuasR" version)) (sha256 (base32 - "1635ff11ahzjrh3cdcxrq5bgd100n444k7mc0maz0jx21vj8qqb1")))) + "0d292xgaq8d3cdpa9anabda03lis46xc29iw9c5k5i3sj7dcr4g5")))) (properties `((upstream-name . "QuasR"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) ("r-biocparallel" ,r-biocparallel) ("r-biostrings" ,r-biostrings) ("r-bsgenome" ,r-bsgenome) -- cgit 1.4.1 From c3ce59c62459076fb3ff84c71bd0bb379b806f65 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:30 +0000 Subject: gnu: r-rqc: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-rqc): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c4da74cc0b..2f89f91ddd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9300,14 +9300,14 @@ quantification of genomic regions of interest.") (define-public r-rqc (package (name "r-rqc") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rqc" version)) (sha256 (base32 - "02hwj2vd003x0zf273ndnwh7kxy6wc3sz14d3kryp2w2aqjj826f")))) + "0hcxkrfja0gmd8r2llijdvaw2xiiplk037305inimz0qna6w2071")))) (properties `((upstream-name . "Rqc"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 505b5d2685cd873e8f87c54c23a732eadd791b28 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:30 +0000 Subject: gnu: r-birewire: Update to 3.26.0. * gnu/packages/bioconductor.scm (r-birewire): Update to 3.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2f89f91ddd..bac4e6ac03 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9343,14 +9343,14 @@ graphics.") (define-public r-birewire (package (name "r-birewire") - (version "3.24.0") + (version "3.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiRewire" version)) (sha256 (base32 - "0p6mr67mkw54490sv4dvkyh8l0xkpjfbqy532vi8l41i40qg3gry")))) + "0ki4rcwjgbixzy5q9s30ajx5zhpl18q50znrb60fchvl4hj9h93w")))) (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 970e3e291e307e25f02f11c96a1b11ac890502c8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:30 +0000 Subject: gnu: r-multidataset: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-multidataset): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bac4e6ac03..0865e004df 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9401,14 +9401,14 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.") (define-public r-multidataset (package (name "r-multidataset") - (version "1.20.2") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiDataSet" version)) (sha256 (base32 - "06wcncz10jm54g0m9yk2314lg8x666p5r4zhi57sp2p50cj1lvnz")))) + "17asldnxqvp3sijx7nbi2lbbgnq4iq8z72qlg9080sm5lga1yy1s")))) (properties `((upstream-name . "MultiDataSet"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 1e2401b767ebdddcd3e6b968d94842419f1d2989 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:30 +0000 Subject: gnu: r-ropls: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-ropls): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0865e004df..43fdbde57d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9438,14 +9438,14 @@ packages.") (define-public r-ropls (package (name "r-ropls") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 - "1j99kdywyljqzdcns5ysh590w4w8iiwzpddpfk5c8d4whax7vk5b")))) + "0mz5lrdsihx66sgx9klnvpxvw1mjjcbijcsdbgxwaimzl9k1kr05")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit 1.4.1 From b960dc7be54319a62db653c97f8efe5f42077921 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:31 +0000 Subject: gnu: r-biosigner: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-biosigner): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 43fdbde57d..4dde77a0ab 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9476,14 +9476,14 @@ coefficients).") (define-public r-biosigner (package (name "r-biosigner") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biosigner" version)) (sha256 (base32 - "159fbkymn92li7dinsm56nsacjp8wnhsljv7airgs9m82p8wd5sl")))) + "189018qahyw33dmg73wa7k4rp8nzrx6ai8f2dr6vhbpcdc1gnm0z")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit 1.4.1 From 4940f6d680a8ebb147f1ca30a7f50a6a8e9b7617 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:31 +0000 Subject: gnu: r-annotatr: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-annotatr): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4dde77a0ab..2161e8d057 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9509,14 +9509,14 @@ datasets.") (define-public r-annotatr (package (name "r-annotatr") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotatr" version)) (sha256 (base32 - "1ls1qdfppcxysggi3bghrnspb5a3s40pm2mj4x0whc7c40cf90mg")))) + "1ha2wn56cdab4p3wdwv4xlqjsgl7sd8phbx71qbclrbdwpq2mi7i")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit 1.4.1 From c58ed007a253eebdcfd7657e60f4b99b73198e0d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:31 +0000 Subject: gnu: r-rsubread: Update to 2.8.0. * gnu/packages/bioconductor.scm (r-rsubread): Update to 2.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2161e8d057..cf3c6bf846 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9550,14 +9550,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.6.4") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "043m4512q73x6q529hqfgrap0fq5anvny4va085nafia06b805pi")))) + "09kd7vl2z9k82ppfzy679hs7d00c60z3w3n6a8wq4z3k3f4glc3s")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) -- cgit 1.4.1 From 311adddab3833b6f48f414ebefd24ffdca7ce808 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:31 +0000 Subject: gnu: r-flowutils: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-flowutils): Update to 1.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cf3c6bf846..501f7a5fa7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9576,14 +9576,14 @@ and to both short and long sequence reads.") (define-public r-flowutils (package (name "r-flowutils") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowUtils" version)) (sha256 (base32 - "1sdwgyvrsz0pp60zdfrcgb7bs8s87j7257p8ck813ydizc324x9w")))) + "0rgybkzbn8c3kpbz0ddghp1np0gka0cgiqvkk5jbnhlgf4s07161")))) (properties `((upstream-name . "flowUtils"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 9e3ee89786e6f824a8cc7f490acf7809e69df325 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:31 +0000 Subject: gnu: r-consensusclusterplus: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-consensusclusterplus): Update to 1.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 501f7a5fa7..d3585e34d3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9602,14 +9602,14 @@ and to both short and long sequence reads.") (define-public r-consensusclusterplus (package (name "r-consensusclusterplus") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ConsensusClusterPlus" version)) (sha256 (base32 - "163nr50nyvwrsajmm0cgxp70pqk61mgw0k7ams694hcb42162j8b")))) + "13z43qbk9z7mvy8v8k185m6n020i6ahb18pm4q88rs75qlklzdkr")))) (properties `((upstream-name . "ConsensusClusterPlus"))) (build-system r-build-system) -- cgit 1.4.1 From 6e07dec942b50f268781c312c13a1006d13c34e0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:31 +0000 Subject: gnu: r-cytolib: Update to 2.6.0. * gnu/packages/bioconductor.scm (r-cytolib): Update to 2.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d3585e34d3..c7c5e27e53 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9627,14 +9627,14 @@ cluster count and membership by stability evidence in unsupervised analysis.") (define-public r-cytolib (package (name "r-cytolib") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 - "0wl7zqwv0i38dfzqfsz40n3mcbxi38ffn1rbd5pm9s7hq16zr4nv")))) + "01r5dfjil1i526kb5gj9c8x9agi90x0bh7lzykbpn0g6s2hznbzi")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) (native-inputs -- cgit 1.4.1 From fe947b3c0eddab772cb0f3877583bd1477d467c7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:31 +0000 Subject: gnu: r-flowcore: Update to 2.6.0. * gnu/packages/bioconductor.scm (r-flowcore): Update to 2.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c7c5e27e53..2212d659bf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9656,14 +9656,14 @@ interact with gated cytometry data.") (define-public r-flowcore (package (name "r-flowcore") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowCore" version)) (sha256 (base32 - "13xpbkxi53rxmhvpdiy6bydmhicmxd2gi96d9c1qx4lkss2f14nc")))) + "0zbd2hrdbb6r0np6nd3ab8nlcf9l57vcwnnhbqkbas8y0c2i2mwp")))) (properties `((upstream-name . "flowCore"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 9e01b4118ef1ccf90747eaa9fe666450750e6194 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:32 +0000 Subject: gnu: r-flowmeans: Update to 1.54.0. * gnu/packages/bioconductor.scm (r-flowmeans): Update to 1.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2212d659bf..12c542323e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9688,14 +9688,14 @@ with flow cytometry data.") (define-public r-flowmeans (package (name "r-flowmeans") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowMeans" version)) (sha256 (base32 - "1awskkq48qhv4v9glxgfqi0kgwqd62fbj641k4vvxfcwsf2c7bfg")))) + "0iy8hvi0inj1ylhdx6q4mya9k55iazprz6fdrnq1mxb2iyndzsl6")))) (properties `((upstream-name . "flowMeans"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 224eccca7ae9b8d15398dda130f39208ab83d852 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:32 +0000 Subject: gnu: r-ncdfflow: Update to 2.40.0. * gnu/packages/bioconductor.scm (r-ncdfflow): Update to 2.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 12c542323e..d2f8d23a29 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9714,14 +9714,14 @@ change point detection.") (define-public r-ncdfflow (package (name "r-ncdfflow") - (version "2.38.0") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ncdfFlow" version)) (sha256 (base32 - "1lm88qnfv6rnnr7wmgbvwyj272imjjjn7h3agxqqzsbmn8vyrnf0")))) + "1c6wb2x24ydqp5nxrx6bhj6f13x9djfy9awkc7zn63xkag7mvvar")))) (properties `((upstream-name . "ncdfFlow"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 833c945998b90fd0b38dccb3d662c6caed61054e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:32 +0000 Subject: gnu: r-ggcyto: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-ggcyto): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d2f8d23a29..4a4dd473ab 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9745,14 +9745,14 @@ manipulation of flow cytometry data.") (define-public r-ggcyto (package (name "r-ggcyto") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggcyto" version)) (sha256 (base32 - "0jd6m84m4znnpix4bcgdby7mnflsn206f5x2vw9n8rxnwzx77wpg")))) + "17dnmsa92gc2za36c3klgd7rklqlxrhkzs5ksnrc1am6a4knc0p1")))) (properties `((upstream-name . "ggcyto"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 3bffe057084d18df11b9650a2af0934dd6f34361 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:32 +0000 Subject: gnu: r-flowviz: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-flowviz): Update to 1.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4a4dd473ab..4500376f49 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9782,14 +9782,14 @@ statistics to the plot.") (define-public r-flowviz (package (name "r-flowviz") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowViz" version)) (sha256 (base32 - "17x04xwyw2pp5zkhgvrmxkb8cbrv9wql6xhjsfpq0n6yd9dxqc1v")))) + "039sh7qn25gp2b34khs8dyrdpxyapsjlprrvxlz8f7dl8gmggl04")))) (properties `((upstream-name . "flowViz"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 007e62be639286d7806d67909dbafa1fa916924b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:32 +0000 Subject: gnu: r-flowclust: Update to 3.32.0. * gnu/packages/bioconductor.scm (r-flowclust): Update to 3.32.0. [inputs]: Remove gsl. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4500376f49..055ae94f33 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9813,14 +9813,14 @@ statistics to the plot.") (define-public r-flowclust (package (name "r-flowclust") - (version "3.30.0") + (version "3.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowClust" version)) (sha256 (base32 - "03xsmprrkxwkaksjlaxwp54mqfb3zlg6dbqhp87w78fwscisv76b")))) + "0ch7mkq40qcnxwgzy51vjdlwyzx4bvp03vpdm6dwjc6qy8a6qfzi")))) (properties `((upstream-name . "flowClust"))) (build-system r-build-system) (arguments @@ -9836,6 +9836,7 @@ statistics to the plot.") ("r-flowviz" ,r-flowviz) ("r-graph" ,r-graph) ("r-mnormt" ,r-mnormt))) + #; (inputs `(("gsl" ,gsl))) (native-inputs -- cgit 1.4.1 From a27ff891a63c95842ee540f772835b7d028094dd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:32 +0000 Subject: gnu: r-rprotobuflib: Update to 2.6.0. * gnu/packages/bioconductor.scm (r-rprotobuflib): Update to 2.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 055ae94f33..2e112acd2f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9854,14 +9854,14 @@ model with Box-Cox transformation.") (define-public r-rprotobuflib (package (name "r-rprotobuflib") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RProtoBufLib" version)) (sha256 (base32 - "1hyds97ay4mn7nl830yh9v8mlasgsljsx5wsrhz2zsmbbyx6wbnb")))) + "04qlhbhdchpr35rdc6jc3y8fy6znnfrdlsb8am04agbrvpjgrx10")))) (properties `((upstream-name . "RProtoBufLib"))) (build-system r-build-system) (arguments -- cgit 1.4.1 From 42df07647aca4df17797efbb3a26673bd7ae1aef Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:33 +0000 Subject: gnu: r-flowworkspace: Update to 4.6.0. * gnu/packages/bioconductor.scm (r-flowworkspace): Update to 4.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2e112acd2f..10ad73f7c2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9883,14 +9883,14 @@ for other R packages to compile and link against.") (define-public r-flowworkspace (package (name "r-flowworkspace") - (version "4.4.0") + (version "4.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowWorkspace" version)) (sha256 (base32 - "1a9qb2dcvwgb3z0vdbbzn1rzy77d3da72kirs272344hdx9b2cx9")))) + "11ni7kgk9s1fz3lvg85s6r7x2fhk4m7cdpilji05ya12jsyr3fig")))) (properties `((upstream-name . "flowWorkspace"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 101cad4791a93cd335da87bcc53ec16dc9ac372d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:33 +0000 Subject: gnu: r-flowstats: Update to 4.6.0. * gnu/packages/bioconductor.scm (r-flowstats): Update to 4.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 10ad73f7c2..b39d442e00 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9937,14 +9937,14 @@ matches the flowJo analysis.") (define-public r-flowstats (package (name "r-flowstats") - (version "4.4.0") + (version "4.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowStats" version)) (sha256 (base32 - "1yr5m7qmhmm52c70z3d0zy4zgf0hja7r2ig9yljv5w86bzm962x6")))) + "0jjfq66m4lbpkynwxaparkd05znhp3jl9ccj37gyghly294x3rm9")))) (properties `((upstream-name . "flowStats"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From b6410270ba77de1582aec4eca670867dd8c8a363 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:33 +0000 Subject: gnu: r-opencyto: Update to 2.6.0. * gnu/packages/bioconductor.scm (r-opencyto): Update to 2.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b39d442e00..b8992fa735 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9973,14 +9973,14 @@ package.") (define-public r-opencyto (package (name "r-opencyto") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 - "1par1d5pk1rjg15q7i5z5wqma7xg6fycb826a823wk8wr52a885x")))) + "11svr1lk383pkm4npwrnf3h37b3drjsmcwcgdbb45x8k2k95z2fm")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 76a0df65d2dfb7aec298fecce878d6da7046d27a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:33 +0000 Subject: gnu: r-cytoml: Update to 2.6.0. * gnu/packages/bioconductor.scm (r-cytoml): Update to 2.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b8992fa735..a4367acac5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10017,14 +10017,14 @@ sequential way to mimic the manual gating strategy.") (define-public r-cytoml (package (name "r-cytoml") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CytoML" version)) (sha256 (base32 - "0ixy7mmnipk8wy61wz6qy7jfbc5zhs6p5iqaii8hdprjnb841ri7")))) + "16rgsc2dz5b8lm3ma8nh9wiknrdnvfjcsij7809rmcfs0gn1arcz")))) (properties `((upstream-name . "CytoML"))) (build-system r-build-system) (inputs -- cgit 1.4.1 From 789958567e06b50d83dbe176536aee54ac3d5e67 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:33 +0000 Subject: gnu: r-flowsom: Update to 2.2.0. * gnu/packages/bioconductor.scm (r-flowsom): Update to 2.2.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a4367acac5..1b951c0b51 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10070,14 +10070,14 @@ standard to exchange gated cytometry data with other software platforms.") (define-public r-flowsom (package (name "r-flowsom") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSOM" version)) (sha256 (base32 - "18h7p7g3w9imyd1c93jllgp4kd74z96cs85wcqfhmd26nx18hl82")))) + "062xrv8li2z849qa8mv5dhafqli6ziz099ikjfvi7v2fr7174p8f")))) (properties `((upstream-name . "FlowSOM"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 765ed6a2c9ccec1a06449398943fdaf7e2d76acc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:33 +0000 Subject: gnu: r-mixomics: Update to 6.17.26. * gnu/packages/bioconductor.scm (r-mixomics): Update to 6.17.26. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1b951c0b51..19d4aae0b3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10113,14 +10113,14 @@ self-organizing map clustering and minimal spanning trees.") (define-public r-mixomics (package (name "r-mixomics") - (version "6.16.3") + (version "6.17.26") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "1x6dbw4q6p9vngm256fr96r9fjxk5nik5ivkhbl5a9zqyq8wagpa")))) + "10ir4876sjmw2mw0cjvshwy3qyhsyz6g1ihyr3dycgzya0jcxw1x")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 20d81fa969f8f22c80e919c15abd21f5c37adb6e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:33 +0000 Subject: gnu: r-depecher: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-depecher): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 19d4aae0b3..c271e43fde 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10159,14 +10159,14 @@ delete entire rows with missing data.") (define-public r-depecher (package ;Source/Weave error (name "r-depecher") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 - "04vxc43p3kpsx0vksk2nwmy9p56h35z2mc8j9p2wm29zaz1y8j3p")))) + "1500jivij7zdycdd0i0b7mgp44w4z0hqnpzqbq8nhvzzdigic8x9")))) (properties `((upstream-name . "DepecheR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 398007448c546d8a5b09f231d7a45e17299e435a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:34 +0000 Subject: gnu: r-rcistarget: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-rcistarget): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c271e43fde..2a9416fad6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10205,14 +10205,14 @@ data, to only emphasize the data that actually matters.") (define-public r-rcistarget (package (name "r-rcistarget") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 - "1yh0l11vnslgr6zsbpgc8mc4aa32zy34f5yrz98hkcdl53iw5y7f")))) + "1qarr7xd71kz1haccj65x7sc7pc4v6xpqcfa3rkyp2bk240gigi7")))) (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 75aed1303ae888f245648193ae860810298b4a14 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:34 +0000 Subject: gnu: r-chicago: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-chicago): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2a9416fad6..6d9f3a1fad 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10247,14 +10247,14 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-chicago (package (name "r-chicago") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Chicago" version)) (sha256 (base32 - "0dkwy6pfvzd7g4qmhjl24ypn92l78w1zy0ajhcxgg39f7zsq883x")))) + "0nz9v37p7zl8yw3ykdbsb3izcwgx349wvrhwfyyn9h3jxjfafngn")))) (properties `((upstream-name . "Chicago"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 6f9be50debd76af9f2f2e9d401dd510736812886 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:34 +0000 Subject: gnu: r-cicero: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-cicero): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6d9f3a1fad..651388b346 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10273,14 +10273,14 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-cicero (package (name "r-cicero") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "1y34cm52bv1v2hr7sz8zjzxwd4wng7v75avz5wx45l0ld54z9l10")))) + "1fc69nkm2cwpr6gkfmra2ph0lrmw486chswp4pn8i70ia43fzdm7")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) -- cgit 1.4.1 From cace0f424b26c7e110a760c0c4b7645cbae37dd8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:34 +0000 Subject: gnu: r-circrnaprofiler: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-circrnaprofiler): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 651388b346..781f609a58 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10340,14 +10340,14 @@ accessibility data.") (define-public r-circrnaprofiler (package (name "r-circrnaprofiler") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "circRNAprofiler" version)) (sha256 (base32 - "1hif40vfg2lkbyf6abbkxbdm3b1biw6gxnh6ca2sydvi3y5l2ys2")))) + "0l83r9idhrha1m21vpnw917m5dlldji49zvx4d25m5g3ia1pkhpf")))) (properties `((upstream-name . "circRNAprofiler"))) (build-system r-build-system) -- cgit 1.4.1 From 26e3242dbadeacc1ffecc7016a419fb0e89191e3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:34 +0000 Subject: gnu: r-genie3: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-genie3): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 781f609a58..b0c9c7fd84 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10475,14 +10475,14 @@ cisTopics and explore the nature and regulatory proteins driving them.") (define-public r-genie3 (package (name "r-genie3") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GENIE3" version)) (sha256 (base32 - "1v54dzcz654wfm3npbp8gb55v49im0fm547cz3hvsidq4zhi3l1b")))) + "0ms769267pimrx3xwwkgjy03qilkxxs7xwhzfca01f65i4n3l6fw")))) (properties `((upstream-name . "GENIE3"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 316bf235c0c534937cdeea51a7236f41e571d5b4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:34 +0000 Subject: gnu: r-roc: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-roc): Update to 1.70.0. [propagated-inputs]: Remove r-knitr. [native-inputs]: Add r-knitr. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b0c9c7fd84..5680acfa79 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10500,17 +10500,17 @@ regulatory networks from expression data.") (define-public r-roc (package (name "r-roc") - (version "1.68.1") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROC" version)) (sha256 (base32 - "1rmsrvn6hrg9ay7xfb05mfkxknnig78p3kbk9ghsd11lhx2fjm3s")))) + "1mgxpv5p6gnv04wzkcryrg5as5xrxvlqlkkcbv0k1bx9y6ykijy9")))) (properties `((upstream-name . "ROC"))) (build-system r-build-system) - (propagated-inputs + (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://www.bioconductor.org/packages/ROC/") (synopsis "Utilities for ROC curves") -- cgit 1.4.1 From f3e1fe2b2f7edfbd8c8faca296f2f4ddc7f5765d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:34 +0000 Subject: gnu: r-watermelon: Update to 2.0.0. * gnu/packages/bioconductor.scm (r-watermelon): Update to 2.0.0. [native-inputs]: Add r-knitr. --- gnu/packages/bioconductor.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5680acfa79..64fe00403f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10548,14 +10548,14 @@ data.") (define-public r-watermelon (package (name "r-watermelon") - (version "1.36.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wateRmelon" version)) (sha256 (base32 - "1qar8z0nf33bqr488swig0bfq8lnvcdjcxvw3q3b0hkkvybn27zw")))) + "1kzkg3cnm5pcs6blpw1qn7na6z3kar93v67680wsxa6qxxdiggk3")))) (properties `((upstream-name . "wateRmelon"))) (build-system r-build-system) (propagated-inputs @@ -10568,6 +10568,8 @@ data.") ("r-matrixstats" ,r-matrixstats) ("r-methylumi" ,r-methylumi) ("r-roc" ,r-roc))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/wateRmelon/") (synopsis "Illumina 450 methylation array normalization and metrics") (description -- cgit 1.4.1 From 0837205009b52dd68e4c06b7dffc2f2ada29d9d8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:35 +0000 Subject: gnu: r-gdsfmt: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-gdsfmt): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 64fe00403f..c855b7c4ed 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10587,14 +10587,14 @@ metrics, with methods for objects produced by the @code{methylumi} and (define-public r-gdsfmt (package (name "r-gdsfmt") - (version "1.28.1") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 - "1w3z718q3bhh8bp71va9pbcd62pwbvgjw33ffg960jya40xssvc7")) + "147i33sb65n3cl3ibmjzgfm7i4ljy640k18mzknvc18v1906j9vp")) (modules '((guix build utils))) ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build ;; them and link with system libraries instead. -- cgit 1.4.1 From 8305dd2411c80d67aea6cc7c7deb3ceb6150e144 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:35 +0000 Subject: gnu: r-bigmelon: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-bigmelon): Update to 1.20.0. [propagated-inputs]: Add r-illuminaio. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c855b7c4ed..d756574a64 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10645,14 +10645,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-bigmelon (package (name "r-bigmelon") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmelon" version)) (sha256 (base32 - "061f0hc4m4nvdr6298pg3inpx1z2bpsm9nlxqs3v7n58q15xyzri")))) + "0ksbmybi8wsg515b4k9ij1xqqk9i90pyap2wq5w3c49qgc0pqali")))) (properties `((upstream-name . "bigmelon"))) (build-system r-build-system) (propagated-inputs @@ -10660,6 +10660,7 @@ with multiple R processes supported by the package @code{parallel}.") ("r-biocgenerics" ,r-biocgenerics) ("r-gdsfmt" ,r-gdsfmt) ("r-geoquery" ,r-geoquery) + ("r-illuminaio" ,r-illuminaio) ("r-methylumi" ,r-methylumi) ("r-minfi" ,r-minfi) ("r-watermelon" ,r-watermelon))) -- cgit 1.4.1 From 10a7837bb8e18f06a22284ea8a1affd7b9366ebf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:35 +0000 Subject: gnu: r-seqbias: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-seqbias): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d756574a64..1353206260 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10674,14 +10674,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-seqbias (package (name "r-seqbias") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqbias" version)) (sha256 (base32 - "06w43plv4x1pafybq633n7adqp9yj3bvaaamq7vylmkfbcx3nl8k")))) + "1q608c1madij8l52ljl3w52vi3cssr6ikny84yj6n8s7yvpx5jpr")))) (properties `((upstream-name . "seqbias"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From bbfeee3ee4b528ffd923f77cdfc0b2cc49c22515 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:35 +0000 Subject: gnu: r-reqon: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-reqon): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1353206260..5f302fb731 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10738,14 +10738,14 @@ injected in that sequence).") (define-public r-reqon (package (name "r-reqon") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReQON" version)) (sha256 (base32 - "1z13avbxwvvhh03arjfnaipznynifsi8k2hzw4kappz24f7lwmza")))) + "14v79vg3pmpkbzgn8xqd020jdwcs8g57d46bzl23yi3w1rsfbrb1")))) (properties `((upstream-name . "ReQON"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From a326c65428cf5bb78321df78b891d3e4e980f9ed Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:35 +0000 Subject: gnu: r-wavcluster: Update to 2.28.0. * gnu/packages/bioconductor.scm (r-wavcluster): Update to 2.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5f302fb731..60af52c080 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10763,14 +10763,14 @@ format.") (define-public r-wavcluster (package (name "r-wavcluster") - (version "2.26.0") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wavClusteR" version)) (sha256 (base32 - "1sydzrqydfv1ik2h08xkxlx6xrv866bf0if6v5wch9l3krh0sych")))) + "1a1zhckrgq5yl51acj5piyh2hq70q6hhpym4cawzdssxhcbq70bk")))) (properties `((upstream-name . "wavClusteR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 8dbca889e0a44b049cf984186f8dea3d2041c082 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:35 +0000 Subject: gnu: r-timeseriesexperiment: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-timeseriesexperiment): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 60af52c080..723ce9843c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10810,14 +10810,14 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).") (define-public r-timeseriesexperiment (package (name "r-timeseriesexperiment") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TimeSeriesExperiment" version)) (sha256 (base32 - "1095a2ynxcf9xiac5cjzslcbmjnjpbby0vy7d84qagdiq1w6mrhn")))) + "0fphnkkd3i7zf33a9lhw95n80vzv1z7fmn7mhrfb949yz4jdvk7d")))) (properties `((upstream-name . "TimeSeriesExperiment"))) (build-system r-build-system) -- cgit 1.4.1 From beb530df2a1eafefe163f078bfc378e11ffb22e9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:36 +0000 Subject: gnu: r-variantfiltering: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-variantfiltering): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 723ce9843c..31684e8552 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10851,14 +10851,14 @@ provides methods for retrieving enriched pathways.") (define-public r-variantfiltering (package (name "r-variantfiltering") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantFiltering" version)) (sha256 (base32 - "0abhrk53csd9jz9sv4q1qr74jax9mbj2icbz1iilf1123nvnjypd")))) + "15js8xzi9rsgkjkqcshzk3r3g85kdnxn5v2hi6l5s4yxj9lnq12p")))) (properties `((upstream-name . "VariantFiltering"))) (build-system r-build-system) -- cgit 1.4.1 From de8a55d138401132eadbbb5d063c0d0d91ead355 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:36 +0000 Subject: gnu: r-variancepartition: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.24.0. [propagated-inputs]: Remove r-colorramps; add r-matrix and r-rlang. --- gnu/packages/bioconductor.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 31684e8552..990081fda7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10957,21 +10957,20 @@ arrays based on fast wavelet-based functional models.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "1pqy2g9pg8pswmkrs2fzlkwwliw2r7f33h05bci5bz41b8ribpzj")))) + "0f5y61dpzwmr8v7npim18zvxa8n49rbzclb9j72haba0px6ibhvw")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocparallel" ,r-biocparallel) - ("r-colorramps" ,r-colorramps) ("r-doparallel" ,r-doparallel) ("r-foreach" ,r-foreach) ("r-ggplot2" ,r-ggplot2) @@ -10981,9 +10980,11 @@ arrays based on fast wavelet-based functional models.") ("r-lme4" ,r-lme4) ("r-lmertest" ,r-lmertest) ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) ("r-pbkrtest" ,r-pbkrtest) ("r-progress" ,r-progress) ("r-reshape2" ,r-reshape2) + ("r-rlang" ,r-rlang) ("r-scales" ,r-scales))) (native-inputs `(("r-knitr" ,r-knitr))) -- cgit 1.4.1 From f61d3ac6ce42060a1c05095422a35eeae72026b7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:36 +0000 Subject: gnu: r-htqpcr: Update to 1.48.0. * gnu/packages/bioconductor.scm (r-htqpcr): Update to 1.48.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 990081fda7..9317791e4f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11002,14 +11002,14 @@ measures.") (define-public r-htqpcr (package (name "r-htqpcr") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HTqPCR" version)) (sha256 (base32 - "1y3ik5a9w66jby6682jfm8mn2883s8yfv4xw8a8v1f6q2d1j938l")))) + "1d7qj5yv6kzqmdrnp5pd8qv1yr4bg8cs39p8ib0i0k8b4wr97kq3")))) (properties `((upstream-name . "HTqPCR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From cdb78e54e6233aaab149e91717409561c4c96244 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:36 +0000 Subject: gnu: r-unifiedwmwqpcr: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-unifiedwmwqpcr): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9317791e4f..1f0f9f66c0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11036,14 +11036,14 @@ features (e.g. genes, microRNAs).") (define-public r-unifiedwmwqpcr (package (name "r-unifiedwmwqpcr") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "unifiedWMWqPCR" version)) (sha256 (base32 - "1clcz610sl3s0mjf84j21xgrmjhkxcc4h292ljwq5yzbkk68g896")))) + "0kw26bm2yyna38q5r4zb2alpa3j4gx7v970419mnjlif4g0hmggk")))) (properties `((upstream-name . "unifiedWMWqPCR"))) (build-system r-build-system) -- cgit 1.4.1 From fcaf2e80ad7c74adb726244eabd6b875fbd43934 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:36 +0000 Subject: gnu: r-universalmotif: Update to 1.12.1. * gnu/packages/bioconductor.scm (r-universalmotif): Update to 1.12.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1f0f9f66c0..5238a58ee5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11061,14 +11061,14 @@ data.") (define-public r-universalmotif (package (name "r-universalmotif") - (version "1.10.2") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "universalmotif" version)) (sha256 (base32 - "0hv2v2zgif5ihr5hxmdz32rln43jc1j0rslp44kd3rijjl45zysn")))) + "0d6zrwbc4i2npl29idm1icwa62wdx47z9s8yx7k662v3qagwpj16")))) (properties `((upstream-name . "universalmotif"))) (build-system r-build-system) -- cgit 1.4.1 From 1feba301d6e371b2fa3243aa082ba906406706fc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:36 +0000 Subject: gnu: r-bgmix: Update to 1.54.0. * gnu/packages/bioconductor.scm (r-bgmix): Update to 1.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5238a58ee5..714b6ae5b2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11175,14 +11175,14 @@ cellular organization in health and disease.") (define-public r-bgmix (package (name "r-bgmix") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BGmix" version)) (sha256 (base32 - "1gp40ddspblpszzm4k4r7ysgx883iwdfqc5ds23p2q1ml9idwgvv")))) + "0x1sx319yfxgkscr9r62msq00ddvmzryzn42wy4dh5pvjmgifkkn")))) (properties `((upstream-name . "BGmix"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 8c6a8a6072a5d05cc981dec78045421e5e666bb5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:37 +0000 Subject: gnu: r-bgx: Update to 1.60.0. * gnu/packages/bioconductor.scm (r-bgx): Update to 1.60.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 714b6ae5b2..d7f6b9d163 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11197,14 +11197,14 @@ gene expression.") (define-public r-bgx (package (name "r-bgx") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bgx" version)) (sha256 (base32 - "18n6j2ihv85rhai5sf5k3mwf9nkc2nl2sinx3rrs6sbl529g4mw4")))) + "0z3isnpyf9s11807dprxmd105lb0k4l7r1sygad30ncjvpldifzm")))) (properties `((upstream-name . "bgx"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 69362a6222439aa71330619d84c385be256f4f6b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:37 +0000 Subject: gnu: r-bhc: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-bhc): Update to 1.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d7f6b9d163..dfbc182e68 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11222,14 +11222,14 @@ Affymetrix GeneChips.") (define-public r-bhc (package (name "r-bhc") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BHC" version)) (sha256 (base32 - "0aaawm7h3ppyyhd7hi14rpynagnxx4730f5vxizj5bpzwbclp6h9")))) + "09nw4ljc9sn7iw09ha0m614hmdjj193xhhav5x5p07l501kks6h2")))) (properties `((upstream-name . "BHC"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BHC/") -- cgit 1.4.1 From afb55b19d4f23eee0358dcd52fa09b4ec8bdb8fd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:37 +0000 Subject: gnu: r-bicare: Update to 1.52.0. * gnu/packages/bioconductor.scm (r-bicare): Update to 1.52.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dfbc182e68..f6a5e2c6b6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11248,14 +11248,14 @@ algorithm which is more efficient for larger data sets.") (define-public r-bicare (package (name "r-bicare") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BicARE" version)) (sha256 (base32 - "0j3gs4xcdgaca2c62jf2h86skbbxm1c9g2khs5bsa8fmkskr6vl9")))) + "1g8vrsc05cysb36gsw8sfmr6dgbh4aji37vcq9qwkmkv3jgvnlf6")))) (properties `((upstream-name . "BicARE"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 4100392b1971d70b6e31ea42e81cba51e31224d4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:37 +0000 Subject: gnu: r-bifet: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-bifet): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f6a5e2c6b6..97015c15dc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11272,14 +11272,14 @@ results.") (define-public r-bifet (package (name "r-bifet") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiFET" version)) (sha256 (base32 - "1fwy7ws0bn67557s0kcw8pbln2jg834n6kfbs8297ps07nxr0lpj")))) + "0vidypvphnj76g4ra5ijrgqx2dnzw0fmvdvz35gsqswrr3k20jkk")))) (properties `((upstream-name . "BiFET"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 66674da16d3ca8d9615a5988d8defe3dbde4aa49 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:37 +0000 Subject: gnu: r-rsbml: Update to 2.52.0. * gnu/packages/bioconductor.scm (r-rsbml): Update to 2.52.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 97015c15dc..746722ad4a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11302,14 +11302,14 @@ the read count and GC content bias.") (define-public r-rsbml (package (name "r-rsbml") - (version "2.50.0") + (version "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rsbml" version)) (sha256 (base32 - "017xwra6ms7kx6sg3ksw1vr9zn23imc2qjgpmjikx7mgbak125xh")))) + "0mdyr637sgasc156cv8i2s2mpl1hdvilfwwkhvw7l95pl90gnsh2")))) (properties `((upstream-name . "rsbml"))) (build-system r-build-system) (inputs -- cgit 1.4.1 From 14b524486ddbd4c72377846320676aab6d794844 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:37 +0000 Subject: gnu: r-hypergraph: Update to 1.66.0. * gnu/packages/bioconductor.scm (r-hypergraph): Update to 1.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 746722ad4a..447ce451ae 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11329,14 +11329,14 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") (define-public r-hypergraph (package (name "r-hypergraph") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hypergraph" version)) (sha256 (base32 - "01knpd964m2g9vwd7c72qnc8g2p2pzhvk7lin4mhvcmb3pvsdlh7")))) + "0xnyl9qh5p32ifvzkcl5g4a38zbnwykqzrp8gwz076a0ksiqqdxf")))) (properties `((upstream-name . "hypergraph"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 2b5e6060278b14b6ca9b7e0ac5b12309a61be77f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:37 +0000 Subject: gnu: r-hyperdraw: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-hyperdraw): Update to 1.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 447ce451ae..11ded1a22c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11351,14 +11351,14 @@ manipulating hypergraphs.") (define-public r-hyperdraw (package (name "r-hyperdraw") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hyperdraw" version)) (sha256 (base32 - "1qkxixkgvvfha0ii8rwwcbrbjmbbxsy8afv5ymcq01k3hbykx44r")))) + "1lkiqrk01hshms9ghsfynxwj69zr3463r3rg8rn7hkwn3bj8xyzj")))) (properties `((upstream-name . "hyperdraw"))) (build-system r-build-system) (inputs `(("graphviz" ,graphviz))) -- cgit 1.4.1 From 8eef74bce101146669e1cdfecd6652a8f6972ea0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:38 +0000 Subject: gnu: r-biggr: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-biggr): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 11ded1a22c..98eeb7818d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11375,14 +11375,14 @@ manipulating hypergraphs.") (define-public r-biggr (package (name "r-biggr") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiGGR" version)) (sha256 (base32 - "1y9659pxm65w51zvrz36girb3qvfc64zijjkxmg6xn4pbc8vv1wf")))) + "1g01666wwznk148776s4vr1hfi3dfl448dhgk4d1qy2wv6sxh9kr")))) (properties `((upstream-name . "BiGGR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 97e275b7b9edbe64f31e15a8eceff12613763ddc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:38 +0000 Subject: gnu: r-bigpint: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-bigpint): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 98eeb7818d..78786aa9cb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11439,14 +11439,14 @@ a file-backed matrix with factor properties.") (define-public r-bigpint (package (name "r-bigpint") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigPint" version)) (sha256 (base32 - "0yrg9x1a92zmz7j5hk77cph1jg82mkpr7k7qi9fdr6z5nqq6fgz6")))) + "0b0l0v9p7a5da3x18d0pqn41ilgxfyzapjaawgsshcfm5mjq5d7q")))) (properties `((upstream-name . "bigPint"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 9e6f77714b88086ecb100938ea8795ceeb26323e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:38 +0000 Subject: gnu: r-chemminer: Update to 3.46.0. * gnu/packages/bioconductor.scm (r-chemminer): Update to 3.46.0. [propagated-inputs]: Add r-jsonlite and r-stringi. --- gnu/packages/bioconductor.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 78786aa9cb..d3df7b3178 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11482,14 +11482,14 @@ visualizing RNA-sequencing datasets and differentially expressed genes.") (define-public r-chemminer (package (name "r-chemminer") - (version "3.44.0") + (version "3.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChemmineR" version)) (sha256 (base32 - "1z59npqk7hnqzhjdnry6lfqlyxfzwqprp7bmbdzs4rp22pzcv1v8")))) + "069xd7if7fs69afmamgl6wrkzpnk97ic6z5ix4vvlzkb078dm0p8")))) (properties `((upstream-name . "ChemmineR"))) (build-system r-build-system) (propagated-inputs @@ -11501,11 +11501,13 @@ visualizing RNA-sequencing datasets and differentially expressed genes.") ("r-dt" ,r-dt) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) + ("r-jsonlite" ,r-jsonlite) ("r-png" ,r-png) ("r-rcpp" ,r-rcpp) ("r-rcurl" ,r-rcurl) ("r-rjson" ,r-rjson) - ("r-rsvg" ,r-rsvg))) + ("r-rsvg" ,r-rsvg) + ("r-stringi" ,r-stringi))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/girke-lab/ChemmineR") -- cgit 1.4.1 From 27791b251763d8b2d3d2360d715fba5e51c103e0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:38 +0000 Subject: gnu: r-bioassayr: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-bioassayr): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d3df7b3178..44ced6aa5a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11525,14 +11525,14 @@ structures.") (define-public r-bioassayr (package (name "r-bioassayr") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioassayR" version)) (sha256 (base32 - "1mlv80w8a7l8cii3dfqvanvh0qdqvcg8c1iiq4xlyvkjxfs64ka1")))) + "1nfp1alva6qim5rbhg9j9w97p2n4z21ghr4j489lqklkcs4d030f")))) (properties `((upstream-name . "bioassayR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 7034456e2c1f698594c192ca9576d53b93315e6d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:38 +0000 Subject: gnu: r-biobroom: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-biobroom): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 44ced6aa5a..d3c35be661 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11560,14 +11560,14 @@ available bioactivity data.") (define-public r-biobroom (package (name "r-biobroom") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobroom" version)) (sha256 (base32 - "1ybyhmrcvj6k1laxw9bc8jbn533frkzh9k8kl1ibd5pi368rfqzn")))) + "034gbywrscv23kk1qnk7sc7dxdckmf60wh29fz65v1n28mkf180r")))) (properties `((upstream-name . "biobroom"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 7ea681d5d526feaba2da35e8238c3384481cf540 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:38 +0000 Subject: gnu: r-graphite: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-graphite): Update to 1.40.0. [native-inputs]: Remove r-knitr. --- gnu/packages/bioconductor.scm | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d3c35be661..ac01aa9797 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11592,14 +11592,14 @@ visualize bioinformatics analyses.") (define-public r-graphite (package (name "r-graphite") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graphite" version)) (sha256 (base32 - "11bgz6951nfygxp3fm0190gf2bb5zplis1bc0am4757liw4qybhf")))) + "0wmdv4j6dinszxwpz2jddshkh1ahbhm2fxh6vhjsk4grw38i1lfr")))) (properties `((upstream-name . "graphite"))) (build-system r-build-system) (propagated-inputs @@ -11608,8 +11608,6 @@ visualize bioinformatics analyses.") ("r-graph" ,r-graph) ("r-httr" ,r-httr) ("r-rappdirs" ,r-rappdirs))) - (native-inputs - `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/graphite/") (synopsis "Networks from pathway databases") (description -- cgit 1.4.1 From 71eae6eabe7a263c6ff20892e33422dcf60bb835 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:39 +0000 Subject: gnu: r-reactomepa: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-reactomepa): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ac01aa9797..4ec7415c68 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11619,14 +11619,14 @@ symbols).") (define-public r-reactomepa (package (name "r-reactomepa") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReactomePA" version)) (sha256 (base32 - "1293z89ai766c559axgr7mz5x4564gyl9xqzf6s8s0aj1xb35gqf")))) + "1f4kd5cql7knnqaq3ba48kkypw8p60lkfdsnpqxcabdj30gqp55b")))) (properties `((upstream-name . "ReactomePA"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 755fd4d87dd8964ec01148b52a85bacb20f032d5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:39 +0000 Subject: gnu: r-ebarrays: Update to 2.58.0. * gnu/packages/bioconductor.scm (r-ebarrays): Update to 2.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4ec7415c68..67625ecd46 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11651,14 +11651,14 @@ enrichment analysis and several functions for visualization.") (define-public r-ebarrays (package (name "r-ebarrays") - (version "2.56.0") + (version "2.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBarrays" version)) (sha256 (base32 - "1k1kl0m7wzaqpv7i20pfav2a6jf93bhri4w7qdikmvkf011n9422")))) + "10dw6c93rmpknzf4cnhw3y7lb27q4xq7x7wirl2a7qywdj0yj2g6")))) (properties `((upstream-name . "EBarrays"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From fa77f4f1541cb4a434151380efa3d3b905402f95 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:39 +0000 Subject: gnu: r-bioccheck: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-bioccheck): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 67625ecd46..1a77ce0ddb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11697,13 +11697,13 @@ monograph.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "1h0l5w33c9jpc20pynq634qmx8jbfa802d7jslmf4haljmrxm4a1")))) + "0w9ddicyp9i8rxf92n9pghd9s6bb8jdjikaylrmkydhb7jbhan0y")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) -- cgit 1.4.1 From 388fa5f0209ceb8310c1d3b1e55b1e398563150f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:39 +0000 Subject: gnu: r-biocgraph: Update to 1.56.0. * gnu/packages/bioconductor.scm (r-biocgraph): Update to 1.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1a77ce0ddb..e34166cafd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11727,14 +11727,14 @@ checks on R packages that are to be submitted to the Bioconductor repository.") (define-public r-biocgraph (package (name "r-biocgraph") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocGraph" version)) (sha256 (base32 - "12bmj9kdlylp02cfwviak7y323ndccl2694rvi4cdg4vsx7v3ya3")))) + "0c7r0c1kx22dlwi6d1ldbkkbf53yi0p3vmgbwzrbkn3cina7bcxq")))) (properties `((upstream-name . "biocGraph"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From d13db6d1c528819da958dd546d942bfb0b5a155c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:39 +0000 Subject: gnu: r-biocstyle: Update to 2.22.0. * gnu/packages/bioconductor.scm (r-biocstyle): Update to 2.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e34166cafd..5ae542a7b3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11752,13 +11752,13 @@ different graph related packages produced by Bioconductor.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.20.2") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "0p2wdq5vrx63ndghl9ww428z2lwnv5y88xmcr51by2g6vcj3brcf")))) + "0xx6xr01sb5wig94515zxgw24r9fv0g962ajy87741civhq32lbd")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) -- cgit 1.4.1 From f1014a64c98ea67898de98107101c50ba91dbeda Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:39 +0000 Subject: gnu: r-biocviews: Update to 1.62.1. * gnu/packages/bioconductor.scm (r-biocviews): Update to 1.62.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5ae542a7b3..ff3e27ac62 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11780,13 +11780,13 @@ functionality.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.60.0") + (version "1.62.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "0pc5ll59vm8a9s1nrdc7p9wk11a52rrz669fsrrqd8qapa8p6wfd")))) + "1v6himzp546dpb990vv0nlya21w8x2x30137rsmahjzg942nzs9r")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) -- cgit 1.4.1 From 2adab7647346df3e2892171ebcf45b6e503c4f91 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:39 +0000 Subject: gnu: r-experimenthub: Update to 2.2.0. * gnu/packages/bioconductor.scm (r-experimenthub): Update to 2.2.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ff3e27ac62..841b12f263 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11808,14 +11808,14 @@ also known as views, in a controlled vocabulary.") (define-public r-experimenthub (package (name "r-experimenthub") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ExperimentHub" version)) (sha256 (base32 - "1mzmw3100lf33yhz27nbxncrjk5bprlackrjcwf8xdhcaidg40p4")))) + "15las4qmqvrn81hczxa3ylikqh54kp1lg9r8rcyfvrx5l0kgwlfq")))) (properties `((upstream-name . "ExperimentHub"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From c208e75fe48039dd67916c3d2ac59a0cf512f47f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:40 +0000 Subject: gnu: r-grohmm: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-grohmm): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 841b12f263..d2d155d6eb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11842,14 +11842,14 @@ access.") (define-public r-grohmm (package (name "r-grohmm") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "groHMM" version)) (sha256 (base32 - "1h63vg1iskw79ijg5h1b9097ams8pp3kvnlawlfci6xfli07xpkj")))) + "1jcj29df4prknqwbydca1jb9w6njacjhwwk9jp0r5mvb88xrm60s")))) (properties `((upstream-name . "groHMM"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From e46b5ad21b28763a8be97f687ff247a3a99693f5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:40 +0000 Subject: gnu: r-multiassayexperiment: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-multiassayexperiment): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d2d155d6eb..2b9f8438d5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11869,14 +11869,14 @@ access.") (define-public r-multiassayexperiment (package (name "r-multiassayexperiment") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiAssayExperiment" version)) (sha256 (base32 - "0l0arf3q1f6zy6pdgsy3h5n523sg1hlilv7lj7snr5814idgdj51")))) + "1h3b8vqlbd04amjprxd1814zksdrbi01a0xn3906vkbqi43hfyn9")))) (properties `((upstream-name . "MultiAssayExperiment"))) (build-system r-build-system) -- cgit 1.4.1 From b9275baa5ad93f0eb616c07707179ff561982bc5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:40 +0000 Subject: gnu: r-bioconcotk: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-bioconcotk): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2b9f8438d5..dc9f3cea29 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11904,14 +11904,14 @@ rownames.") (define-public r-bioconcotk (package (name "r-bioconcotk") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocOncoTK" version)) (sha256 (base32 - "1ix09a39z7y2cj0y8qsd66ka8a8y8q79w08l4jv1yhhn9h4va89s")))) + "1h5s6wbc5n5x5d28rynxpcmaklxdhf72g9gg9fy8cg77niipvxd9")))) (properties `((upstream-name . "BiocOncoTK"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From a6dd46bfc5f0144a63401e0a2fa029bf33771c7c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:40 +0000 Subject: gnu: r-biocor: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-biocor): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dc9f3cea29..3f394b28dc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11949,14 +11949,14 @@ tools for genome-scale analysis of cancer studies.") (define-public r-biocor (package (name "r-biocor") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioCor" version)) (sha256 (base32 - "135rga7mwpzy8ypvriqpbmlh9l5yf61s9s1sa9615qfab14jh06b")))) + "0ii4g7438lb34ykidkbxw3v3k289k662rgbgayf9gak5avpkb2cq")))) (properties `((upstream-name . "BioCor"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From b2253e6ceb59459753a4129f5c513471ba09b935 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:40 +0000 Subject: gnu: r-biocpkgtools: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-biocpkgtools): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3f394b28dc..8c12c67a41 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11978,14 +11978,14 @@ gene selection, testing relationships, and so on.") (define-public r-biocpkgtools (package (name "r-biocpkgtools") - (version "1.10.2") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocPkgTools" version)) (sha256 (base32 - "1sfp1nxlwbbbpx2iwvyk9p10jdy2vxhgn2b5fy5blayzjjlb3d80")))) + "13m6h35938407ajj7fakl50g4p2wsvinkg0r2mwl1zwq88735arg")))) (properties `((upstream-name . "BiocPkgTools"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 2e0b3797af93f8f4900f1a5c81b7d180cc0fd7d9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:40 +0000 Subject: gnu: r-biocset: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-biocset): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8c12c67a41..9cd0fcb07a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12026,14 +12026,14 @@ analytics on packages.") (define-public r-biocset (package (name "r-biocset") - (version "1.6.1") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSet" version)) (sha256 (base32 - "0nmrg9cgq8l9w467y364jghnvym05abpj8pyj90grmrib2xc5sj2")))) + "0ysm68gcalg3d91jx6vmdzra01vc6kvzqnvz557g3rnm0wkx12q6")))) (properties `((upstream-name . "BiocSet"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From b9c74b05d766b29be8d9bbccb8074f76d7cc95cf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:40 +0000 Subject: gnu: r-biocworkflowtools: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-biocworkflowtools): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9cd0fcb07a..cfa9f921df 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12064,14 +12064,14 @@ accessing web references for elements/sets are also available in BiocSet.") (define-public r-biocworkflowtools (package (name "r-biocworkflowtools") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocWorkflowTools" version)) (sha256 (base32 - "1a32bwgnxaw0gv2gij2p4rm0a6l06jjhidvfz2v4k900pz1w79av")))) + "1j9s8w5y8savcmh70npkanxacq1kipxnwk1wsiw5hwnp1p13ldaa")))) (properties `((upstream-name . "BiocWorkflowTools"))) (build-system r-build-system) -- cgit 1.4.1 From b24de9bf77cbf013f65f594f2a4af45c91580732 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:41 +0000 Subject: gnu: r-biodist: Update to 1.66.0. * gnu/packages/bioconductor.scm (r-biodist): Update to 1.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cfa9f921df..3a3a046463 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12097,14 +12097,14 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") (define-public r-biodist (package (name "r-biodist") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioDist" version)) (sha256 (base32 - "1y1x9q9aa76gbhsyfn638rxp5icjvq30fv3a4205xh7g5jwlf6yw")))) + "0y35c9sdq5x4q64ip0wgqz59mh01l71k1pp6n8vqbr667nwg0gdp")))) (properties `((upstream-name . "bioDist"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From af5ff34f24cc9751b446bf39d19d60aa4d008c57 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:41 +0000 Subject: gnu: r-pcatools: Update to 2.6.0. * gnu/packages/bioconductor.scm (r-pcatools): Update to 2.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3a3a046463..5af62dd61c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12120,14 +12120,14 @@ distance measures.") (define-public r-pcatools (package (name "r-pcatools") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "PCAtools" version)) (sha256 (base32 - "11idi9fwvyhkakbm63qxcdhkany8gbskis04z0p5a39lppq8ks31")))) + "10kfhsxhsjpzal3yvcqg769h5fz99cqqjq217cj9jip3jfh2m2h4")))) (properties `((upstream-name . "PCAtools"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 1be95ea42592e70d67c5690a7f4b083fa2cee344 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:41 +0000 Subject: gnu: r-rgreat: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-rgreat): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5af62dd61c..db6ab808ee 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12166,14 +12166,14 @@ dimensional mass cytometry data.") (define-public r-rgreat (package (name "r-rgreat") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGREAT" version)) (sha256 (base32 - "0ads9c9i8b39wvjih057zlyivj8zpsqjxf6r97yflz4sbi1jmcji")))) + "0kr61mhxp9phn1136fci450zwfhsipchmlm8d5rgib4lh0zbxrhl")))) (properties `((upstream-name . "rGREAT"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 0d62874ccf45a809bd78c8beada081657c550440 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:41 +0000 Subject: gnu: r-m3c: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-m3c): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index db6ab808ee..8f72056a65 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12194,14 +12194,14 @@ user's input and automatically retrieving results from GREAT web server.") (define-public r-m3c (package (name "r-m3c") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "M3C" version)) (sha256 (base32 - "17gj4haa4ywc6bmppm342jzppl3inqa94235yspikij6c098vrmc")))) + "0jsql5wd58hs5mnn9wq5b4kl3z57y6amykirfb3k047zpyi8ijnh")))) (properties `((upstream-name . "M3C"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From fdf61867d6ef0d12849995a04c7f77ad39aa34ff Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:41 +0000 Subject: gnu: r-icens: Update to 1.66.0. * gnu/packages/bioconductor.scm (r-icens): Update to 1.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8f72056a65..95ef8ca193 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12227,14 +12227,14 @@ hypothesis @code{K=1}.") (define-public r-icens (package (name "r-icens") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Icens" version)) (sha256 (base32 - "1rzgwxx4w2bqsaz0xmkhi4w9zsxgms80xf59zg1xp1camyhaihlz")))) + "08jd7g28mazvwd3qbq8y26czmkz45avp4vy8l7i5d6qajwzqzgzs")))) (properties `((upstream-name . "Icens"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 51f9943d1e76ccf90b788e215562b7da82b7ecd2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:41 +0000 Subject: gnu: r-preprocesscore: Update to 1.56.0. * gnu/packages/bioconductor.scm (r-preprocesscore): Update to 1.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 95ef8ca193..b5bc0f0aa2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12357,14 +12357,14 @@ generated.") (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "17a00blz4kvhmsk92bp5alj9kdpy7h1id7nk4vqxakhkb2jabr20")))) + "1i93vdqa6pwzamiryp3lv6cyvhx9shs01is0q6vbmdvcbii2vf3x")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) -- cgit 1.4.1 From 1417f1171cecf68d15844378ac89765c3fffcaa1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:41 +0000 Subject: gnu: r-s4vectors: Update to 0.32.0. * gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b5bc0f0aa2..4051c9d846 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12378,13 +12378,13 @@ routines.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.30.2") + (version "0.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "0n13j8fkiy8b071wvwwh3ip9cvq22f74hb1msx91mdab2xl47zxs")))) + "1zm1xlqrq1f9xa81j3ij2p78g3aywq7izsk3h40z94fjggahvc09")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) -- cgit 1.4.1 From 7752397cf1f46fb7f723fcf92c7ff41209050c4f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:42 +0000 Subject: gnu: r-rgraphviz: Update to 2.38.0. * gnu/packages/bioconductor.scm (r-rgraphviz): Update to 2.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4051c9d846..996a53e0c6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12445,14 +12445,14 @@ data manipulation and visualization.") (define-public r-rgraphviz (package (name "r-rgraphviz") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rgraphviz" version)) (sha256 (base32 - "0d0xq1vgr4b165cn4wg7zmfjyc1d9ir4amgs196j4cgrhpmrnl8s")))) + "0fyv1ybpahkwz3fawzxgxfnshi8y7c18262rgdmqwdl5662vv1p7")))) (properties `((upstream-name . "Rgraphviz"))) (build-system r-build-system) (arguments -- cgit 1.4.1 From 2603747a560d8d6b8914ed75ebec208bcd8d2a4b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:42 +0000 Subject: gnu: r-fithic: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-fithic): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 996a53e0c6..381fc7118f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12483,13 +12483,13 @@ objects from the @code{graph} package.") (define-public r-fithic (package (name "r-fithic") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FitHiC" version)) (sha256 (base32 - "1p8a6lis5yswaj647bjw89harlarnsxmvjzz63fn1l6gxrwhh8bx")))) + "0a3d2bxp98lmbf3i864zgfwxwvxyqfcrh75z9yz7ra7y44pkjr4y")))) (properties `((upstream-name . "FitHiC"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 77450726d63e619845472ef1b1317c614601d0bc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:42 +0000 Subject: gnu: r-hitc: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-hitc): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 381fc7118f..5329c54c34 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12509,13 +12509,13 @@ assays such as Hi-C.") (define-public r-hitc (package (name "r-hitc") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HiTC" version)) (sha256 (base32 - "0s3kfqs3zlmq61hxdmxpmi9gfs9w3byckw7xzp1hrhdbsl46yvgq")))) + "1ckiwqfq86k8p3y36iwr7k3y6g4z80n8hb047c0i2491lrn23rhx")))) (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 6f2d0551f1d2f71f1d6861683374f0848c22902d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:42 +0000 Subject: gnu: r-hdf5array: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-hdf5array): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5329c54c34..b1ba33ad7f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12538,14 +12538,14 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "1718hplz5qlbwxwb87509bl7lir9kilvn1s7p2haz551pg48zvrc")))) + "13h6qr4zkynir0ck2aiasjvlid7hrk3m2lzkjyhpvbg1a15r8zi9")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs -- cgit 1.4.1 From 29111142d1fbec5d0aea8fc6dfcab4e760fa0c4a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:42 +0000 Subject: gnu: r-rhdf5lib: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-rhdf5lib): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b1ba33ad7f..a4ac0be20a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12569,14 +12569,14 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.14.2") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "1cwynbcaaxmbh45fc0d264liqdj0wbjlj7k2bsq3qfjbnh6kkam5")) + "0yly9s3wdnhd9ci2jxfkql38ibv35yzs38a6g6ashbg1m5kgwd9p")) (modules '((guix build utils))) (snippet '(begin -- cgit 1.4.1 From 756f5411a98e250653dd76abf78e4f48b4d408d5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:42 +0000 Subject: gnu: r-beachmat: Update to 2.10.0. * gnu/packages/bioconductor.scm (r-beachmat): Update to 2.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a4ac0be20a..69bfcec150 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12652,14 +12652,14 @@ packages.") (define-public r-beachmat (package (name "r-beachmat") - (version "2.8.1") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 - "06bpfpddsl49csxrs8hlx5pv0absc2wdcparchf8qqaqydazwci2")))) + "1l8c9q35mf90ckb366bcfqa0v2gw7ahs2h362j7cwv8fp39h4mpb")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) -- cgit 1.4.1 From d6130127e8098f85f166dbfbd2baa06bb9655980 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:43 +0000 Subject: gnu: r-cner: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-cner): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 69bfcec150..56a1bf40a1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12681,13 +12681,13 @@ matrices.") (define-public r-cner (package (name "r-cner") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CNEr" version)) (sha256 - (base32 "13w0gsfm7k29dp5nb0c9sb2ix506ph6dixsjis6xxcz6acq7lg2k")))) + (base32 "0w4iqmyyhsb6l9bi8c6qwdh4j6z2i1i5fi85ia9069fpl9d0hpl2")))) (properties `((upstream-name . "CNEr"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) -- cgit 1.4.1 From d15fac371309fabf5f776e0576bd5cb8277b23b1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:43 +0000 Subject: gnu: r-tfbstools: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-tfbstools): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 56a1bf40a1..4cc62240b6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12729,14 +12729,14 @@ advanced visualization of sets of conserved noncoding elements.") (define-public r-tfbstools (package (name "r-tfbstools") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TFBSTools" version)) (sha256 (base32 - "1avgjv2nyr28cla0z9dvh3v0hr1f561sz2as1k53a42irbjk0var")))) + "0j5gv145fczzdspwhbywlg47y05pgnkra9jg7bn4wa1k0cf5pr9g")))) (properties `((upstream-name . "TFBSTools"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 5eb0f4d20ea1ff6098ec981dac25b3d0d89b124c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:43 +0000 Subject: gnu: r-motifmatchr: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-motifmatchr): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4cc62240b6..b926d4a68a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12775,14 +12775,14 @@ provides a wrapper of de novo motif discovery software.") (define-public r-motifmatchr (package (name "r-motifmatchr") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifmatchr" version)) (sha256 (base32 - "1vif3dp4lv4jz1pxsq0ig791ir8q65jmrlqmkyfxpfxfj5alqnbm")))) + "0f7j54zdn51h1gcn81vqs8avmschjwqprjcfpvsi00q4fna3fg7z")))) (properties `((upstream-name . "motifmatchr"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 9f7327588df1d3c89453d679ce9c9474fac1d33a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:43 +0000 Subject: gnu: r-chromvar: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-chromvar): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b926d4a68a..7f3e095d5d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12809,13 +12809,13 @@ This package wraps C++ code from the MOODS motif calling library.") (define-public r-chromvar (package (name "r-chromvar") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromVAR" version)) (sha256 - (base32 "1birmwvcvl2hb5ygbsb3wvbdfayqqs53j1bks46cbkq7ybigfyar")))) + (base32 "0ylsfr540l763bh010irbcavlskahyb1769pppimdgn22gyr3spk")))) (properties `((upstream-name . "chromVAR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From c7b54ba02638119194e0896ec68a9e59ce5e83b9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:43 +0000 Subject: gnu: r-singlecellexperiment: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-singlecellexperiment): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7f3e095d5d..3966e78901 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12856,14 +12856,14 @@ sequence (@code{DNAse-seq}) experiments.") (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleCellExperiment" version)) (sha256 (base32 - "1bwdhx0ss0s8f4xdgwd7x48apn849x4dyb5hbyglcz31r5vh1qgz")))) + "01075vbs8hy399pxalav9rbkz4djvl84ip559jkz51fypd0m4i39")))) (properties `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) -- cgit 1.4.1 From 08defd9cdb32a20d5dc083cf1c903549f95501c7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:43 +0000 Subject: gnu: r-scuttle: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-scuttle): Update to 1.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3966e78901..0f64350e09 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12887,14 +12887,14 @@ libraries.") (define-public r-scuttle (package (name "r-scuttle") - (version "1.2.1") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scuttle" version)) (sha256 (base32 - "015k879gg2r39lp6mz26jwmysa56k0ial6v74zzmbi8hnz9zic3i")))) + "1dbdb6yc6wk01dljy1vy6f0lf44crc5rxxnc4bhjk8i4iljz8467")))) (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 980e6af8aa4e92a3fa27b680c2094a454859c984 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:44 +0000 Subject: gnu: r-scater: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-scater): Update to 1.22.0. [propagated-inputs]: Add r-ggrepel. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0f64350e09..46c93d5dbb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12922,13 +12922,13 @@ of other packages.") (define-public r-scater (package (name "r-scater") - (version "1.20.1") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "1046fgf93dda3y2z5ilrjdczz7klj67ag63p4p1h03965wpj9vfn")))) + "0k4i9pwmwxcr5a40ljl27wriccwn5vc52xy48yjjh8ppl5dbggdg")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) @@ -12940,6 +12940,7 @@ of other packages.") ("r-delayedmatrixstats" ,r-delayedmatrixstats) ("r-ggbeeswarm" ,r-ggbeeswarm) ("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) ("r-gridextra" ,r-gridextra) ("r-matrix" ,r-matrix) ("r-rcolorbrewer" ,r-rcolorbrewer) -- cgit 1.4.1 From e4cfcbfda32447e8ca47f5c41ebf897e71b8d2cc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:44 +0000 Subject: gnu: r-scran: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-scran): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 46c93d5dbb..a5befb3624 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12963,14 +12963,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.20.1") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "0ilzp6ngw9pq88gk79iic2zxfh5jaic6lnq3xfwc9a269bjylff0")))) + "1nyvbss4914giwzp5wiw9g4z5b6lr5iprbjrqlg4vpgnf1hz8k7l")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) -- cgit 1.4.1 From de38a03f61d6719bf71f8ef4a3b943fffc495fba Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:44 +0000 Subject: gnu: r-sparsematrixstats: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-sparsematrixstats): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a5befb3624..2e685f6eed 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13006,14 +13006,14 @@ variable and significantly correlated genes.") (define-public r-sparsematrixstats (package (name "r-sparsematrixstats") - (version "1.4.2") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sparseMatrixStats" version)) (sha256 (base32 - "0b22kzg751zlkcbs8pi0bcqrsj3imsg35qfvxfrqb7gav7qznc8v")))) + "0ifqj4a6mn4749sr62gq3dwd6mmbbzdx5mh5b5663vcgl1kw96x1")))) (properties `((upstream-name . "sparseMatrixStats"))) (build-system r-build-system) -- cgit 1.4.1 From 5c75a6d18e06f6262544eb79edd1d494db5804aa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:44 +0000 Subject: gnu: r-delayedmatrixstats: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2e685f6eed..123b1bc813 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13034,14 +13034,14 @@ data in the column sparse format.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.14.3") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "1zxs2wjnsq9w1cl4andsd7y9xsdnl1an55khw9viaq758m7hhbcn")))) + "1pqwkk39rfhcnhmgchk0gfmm4jgasl19yq0nhhwsfj45y2vk6kjk")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) -- cgit 1.4.1 From ffcb3606d0b241a5800bd914a815b587cf7dd0af Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:44 +0000 Subject: gnu: r-mscoreutils: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-mscoreutils): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 123b1bc813..1f186bdeac 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13070,14 +13070,14 @@ memory usage and processing time is minimized.") (define-public r-mscoreutils (package (name "r-mscoreutils") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MsCoreUtils" version)) (sha256 (base32 - "13g8a726vsyjs6m1kd42vf8avdnmhykxhl6z3j2njzkp2jg17pd8")))) + "1w8d1v2r3plwwcz23zhbpvklhapf2a6x3xmglyh4sh6sy9ynkgrv")))) (properties `((upstream-name . "MsCoreUtils"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 2de21518f1f447e19dcad36875e52d89ca5a8e66 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:44 +0000 Subject: gnu: r-biocio: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-biocio): Update to 1.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1f186bdeac..97dd1cfe3e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13134,14 +13134,14 @@ the respective packages (such as e.g. @code{xcms}).") (define-public r-biocio (package (name "r-biocio") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocIO" version)) (sha256 (base32 - "0skwnpxl6fkqihidpqrfzzh7b05x11j6jwkiinmhggmv0ggjb5ph")))) + "1qg6v961sbj7qwyjx4z720f6h0kq693p7gc8q99my7gqkbbcxrfr")))) (properties `((upstream-name . "BiocIO"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 357c74ef3e7001c66948a933fd355d279c5cdc23 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:44 +0000 Subject: gnu: r-msmseda: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-msmseda): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 97dd1cfe3e..65bcbc71f3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13168,14 +13168,14 @@ as well as local access. Developers can register a file extension, e.g., (define-public r-msmseda (package (name "r-msmseda") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsEDA" version)) (sha256 (base32 - "0555a3riyp781mlffmnf93igfq8vl8wjk51pa9qb48qkdn6y8pfc")))) + "1jammjkjjkcqad2ki02l2pdf4jybyh71hv463aya2ylmzsin5vi9")))) (properties `((upstream-name . "msmsEDA"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 9df8fa7b387644e2e524d1699d0f0ff0ac27d2a2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:45 +0000 Subject: gnu: r-msmstests: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-msmstests): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 65bcbc71f3..a203cbb940 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13194,14 +13194,14 @@ experiments, and visualize de influence of the involved factors.") (define-public r-msmstests (package (name "r-msmstests") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsTests" version)) (sha256 (base32 - "11vhy1l6za73dpdj85q4ksaghgd8vb2h8v9iirmsn2vpajqrvgjh")))) + "0xmjgd8rqpb8i7d46pvnj7da2di8bwfdncr48b8hgylkc98ghznb")))) (properties `((upstream-name . "msmsTests"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From eed4a322f105b4175114f84a7c31ced0ee41baa8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:45 +0000 Subject: gnu: r-catalyst: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-catalyst): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a203cbb940..2ff10093d0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13226,14 +13226,14 @@ relevant, and the minimum expression of the most abundant condition.") (define-public r-catalyst (package (name "r-catalyst") - (version "1.16.2") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CATALYST" version)) (sha256 (base32 - "1vw8x54hwgcyn29k81zcvawawy2iy2qgp49gjpb830q04gx6yc6h")))) + "15lah45lf16zh1ankbpjvz8zp38lldvq074nmvb99rhhqys2gbgi")))) (properties `((upstream-name . "CATALYST"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From b1de4e61a050430b1a09677d3f35e45c5ce9baf1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:45 +0000 Subject: gnu: r-erma: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-erma): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2ff10093d0..46f92fb9d1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13284,14 +13284,14 @@ standards, ii) single-cell deconvolution, and iii) bead-based compensation.") (define-public r-erma (package (name "r-erma") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "erma" version)) (sha256 (base32 - "02a9702sasgighwb0f9ii8n30ngfx1hjnppaay1f5zsigr8vqalz")))) + "0pb9ar1wy613vg6sfdmn8n4cfv1328m8bagnigsjdb3hc3hbir4z")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit 1.4.1 From 6d193b32887f180af1205ad4bf94ad1e0394f805 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:45 +0000 Subject: gnu: r-ggbio: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-ggbio): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 46f92fb9d1..a084efa5f7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13324,14 +13324,14 @@ by Ernst and Kellis.") (define-public r-ggbio (package (name "r-ggbio") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 - "0k3dxacrwgyrkvm7ggc2s1s1pbfs6c0a7ngykkj7jnc73czvnilx")))) + "1svmjaa3gisi39sl52337drvd54havcy5pjmwrykgykz5flid2m7")))) (build-system r-build-system) (arguments `(#:phases -- cgit 1.4.1 From 38a7f293743dd2c2e55d3b28d42bad1ec7e4fecd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:45 +0000 Subject: gnu: r-gviz: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-gviz): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a084efa5f7..66b470de84 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13492,14 +13492,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.36.2") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "0lp0k8jd4dfsfn10706124graaqnzcyv1siblvm8dn2ykw2rc6vl")))) + "0nqa7m300d7gpsayb6c6rv64d3y8c390wvwgz7v29zs9c025s9a8")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From ab00f1b61c1328e56ddf12df805540c03cd4d074 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:45 +0000 Subject: gnu: r-gwascat: Update to 2.26.0. * gnu/packages/bioconductor.scm (r-gwascat): Update to 2.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 66b470de84..bc9b53957c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13541,14 +13541,14 @@ with your data.") (define-public r-gwascat (package (name "r-gwascat") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gwascat" version)) (sha256 (base32 - "0109cxsviq1sk5hfwkjzd0y1kpm934287asjjd0j8jhh4b0ah2b2")))) + "0s67jgk3gnfiyfjwhq4r5xlfnip29blis4fg75kn4qmvjv5j2pxx")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit 1.4.1 From 7b6b39bd970e270c89753868118b498ecf89756f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:45 +0000 Subject: gnu: r-kegggraph: Update to 1.54.0. * gnu/packages/bioconductor.scm (r-kegggraph): Update to 1.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bc9b53957c..844f6c9b7b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13575,13 +13575,13 @@ EMBL-EBI GWAS catalog.") (define-public r-kegggraph (package (name "r-kegggraph") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGgraph" version)) (sha256 - (base32 "0zxdph5hzr3kzj2g1mjqpiviwa189a5sq4bw7wiry6r79fdnklqs")))) + (base32 "1qqvbv1sq9j570syb2802ya2ffg1k8f1w986wr6ksqkwxb9qbbm4")))) (properties `((upstream-name . "KEGGgraph"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From a8fb8beb311899f92cf4eccf80aa4c002045bdc7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:46 +0000 Subject: gnu: r-ldblock: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-ldblock): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 844f6c9b7b..b8aa45d263 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13602,14 +13602,14 @@ functionalities including parsing, graph operation, visualization and etc.") (define-public r-ldblock (package (name "r-ldblock") - (version "1.22.1") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "16vp5psmigxdkkd6fbivb6s8mvd7rsnm771wsbjvayl2y7ig7kq4")))) + "1v9b372d5hpwwik6956mfwc9b3bibygz042i4nydsklnbwm5vcmg")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) -- cgit 1.4.1 From ce510880ecff4b278348275d8cb9ce73baa1c34b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:46 +0000 Subject: gnu: r-pathview: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-pathview): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b8aa45d263..d14896ea4b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13728,13 +13728,13 @@ other functional sequencing data.") (define-public r-pathview (package (name "r-pathview") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pathview" version)) (sha256 - (base32 "1fank0qavv9ikmzxvms8mky2wbzny02rfqkvsqzma26r3vl4r1g1")))) + (base32 "1jdl81lvrsz03b1nws90nssf2clipipzaqvwm1pq57mvshnlnkjr")))) (properties `((upstream-name . "pathview"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 41c4e6391d2b0fe09d4b08653d7828c0331fcc0e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:46 +0000 Subject: gnu: r-snpstats: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-snpstats): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d14896ea4b..27f48b2af1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13762,14 +13762,14 @@ large-scale and fully automated analysis.") (define-public r-snpstats (package (name "r-snpstats") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "snpStats" version)) (sha256 (base32 - "11vvih5y9kvyjfp2navkfpp4xiyfgwlv4r0x3p52hkj92pc2pg3g")))) + "0ha34b5cg26940xihgky45adns1nflrgq2qjq77w4bncxpaacsqq")))) (properties `((upstream-name . "snpStats"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) -- cgit 1.4.1 From 97c0e316d3e2b5b22a92b20a85f9dc31f0faafa7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:46 +0000 Subject: gnu: r-chromstar: Update to 1.19.0. * gnu/packages/bioconductor.scm (r-chromstar): Update to 1.19.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 27f48b2af1..33158531bf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13789,14 +13789,14 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.") (define-public r-chromstar (package (name "r-chromstar") - (version "1.18.0") + (version "1.19.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromstaR" version)) (sha256 (base32 - "09cqzylci4x4i7wn4ckcqhdlljbzfrp08wdvkkc5vrdldnj9pq5h")))) + "0z511l26fhz00qn8h2yybylk8c3ws8hj1hp8hq9qj9mfczwiqy3j")))) (properties `((upstream-name . "chromstaR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From c7641e432762fdf587e1600c0d4cbad390af2f45 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:46 +0000 Subject: gnu: r-guitar: Update to 2.10.0. * gnu/packages/bioconductor.scm (r-guitar): Update to 2.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 33158531bf..42567faabb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13827,14 +13827,14 @@ analyses.") (define-public r-guitar (package (name "r-guitar") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Guitar" version)) (sha256 (base32 - "1q4m6c5181dw12lvdp324jlk78c9jgcsg6b9hk87zjadp6j0gfr6")))) + "082yja4mmsq77sllv3c88agxjbb6jxwil2krb8fkfsijvyyx11c9")))) (properties `((upstream-name . "Guitar"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 558abe3b47e46caec38d33246f02e6bc31a53295 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:46 +0000 Subject: gnu: r-sushi: Update to 1.31.0. * gnu/packages/bioconductor.scm (r-sushi): Update to 1.31.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 42567faabb..54a5fe1b4e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13859,13 +13859,13 @@ starting site, start codon, stop codon and transcription ending site.") (define-public r-sushi (package (name "r-sushi") - (version "1.30.0") + (version "1.31.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Sushi" version)) (sha256 (base32 - "1m5l0nflhcynb3gz7b8qzvknb0s6xhds8z1yl3mbv8ic9qn2knv4")))) + "1cj4palsq99vnwihp6z9mw0f8w9qj2vq8zwnabf3bgg0l1wpsc7c")))) (properties `((upstream-name . "Sushi"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 7ed7b40b18c2a823cc34de86e2e4faac295afd01 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:46 +0000 Subject: gnu: r-ballgown: Update to 2.26.0. * gnu/packages/bioconductor.scm (r-ballgown): Update to 2.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 54a5fe1b4e..1fd30b91c2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13881,14 +13881,14 @@ visualizations for publication-quality multi-panel figures.") (define-public r-ballgown (package (name "r-ballgown") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ballgown" version)) (sha256 (base32 - "0ff8z4pfgzai2q4aafclg36bhsi9jwl9xhh1p9fqhmikisscq7i1")))) + "0fiky82arvgzgxrm4bqn74m5kngqpdaqf6ks4cr89nlnhfq0v6rf")))) (properties `((upstream-name . "ballgown"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 8dd33b890a0feee915d7ad75e6a9e6e000deb8de Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:47 +0000 Subject: gnu: r-megadepth: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-megadepth): Update to 1.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1fd30b91c2..a709532573 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13915,14 +13915,14 @@ to annotation.") (define-public r-megadepth (package (name "r-megadepth") - (version "1.2.3") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "megadepth" version)) (sha256 (base32 - "0grgj7bzyqnxby0sx5ic1h9bzmx19xwl0a5b3v6wbnwqcla2i3kg")))) + "0mg7n3990qv65rg624473ssccka0yjpgc20glrdc5saci891j44r")))) (properties `((upstream-name . "megadepth"))) (build-system r-build-system) (inputs `(("megadepth" ,megadepth))) -- cgit 1.4.1 From 744c9f435178898fa8bd130f6c81356f255f1bd2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:47 +0000 Subject: gnu: r-beclear: Update to 2.10.0. * gnu/packages/bioconductor.scm (r-beclear): Update to 2.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a709532573..05998a4991 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13948,14 +13948,14 @@ regions or annotations of your choice from BigWig files.") (define-public r-beclear (package (name "r-beclear") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BEclear" version)) (sha256 (base32 - "0w18livng2gcmjgvws7pix3gsnj237rs34sgwxsfmn8p5vfx8b30")))) + "1njb1lfd4wmsrfw06jc8z8vdk14nmcw9lwyvbxr7z1zg4h8v6c29")))) (properties `((upstream-name . "BEclear"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From bdb55dcdf7e05765673c6eb1f9886ee272a74fcc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:47 +0000 Subject: gnu: r-bgeecall: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-bgeecall): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 05998a4991..b400003212 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13981,14 +13981,14 @@ real numbers.") (define-public r-bgeecall (package (name "r-bgeecall") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BgeeCall" version)) (sha256 (base32 - "1byciy7vzbdkdgaim10s9qb7zlxsywbhcsrka31gm0rm9ljqc665")))) + "0rbbl8m48qcvl26lnf27jq108p7pi84m9ac3qcpjc0ax5wywbv16")))) (properties `((upstream-name . "BgeeCall"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From b223a11c4108f5f1e8fb1a9ccbfa58a4040ef65b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:47 +0000 Subject: gnu: r-bgeedb: Update to 2.20.0. * gnu/packages/bioconductor.scm (r-bgeedb): Update to 2.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b400003212..be182a77b9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14017,14 +14017,14 @@ all RNA-Seq libraries of each species integrated in Bgee.") (define-public r-bgeedb (package (name "r-bgeedb") - (version "2.18.1") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BgeeDB" version)) (sha256 (base32 - "1ziq180yfpdqwhjdzkwjjhwzn3kb0gkj6q0a26c7a30mcfb50w11")))) + "0pjymal01sjl5dc37g66wykgxnksarlbvwnbvhg7w0i7y92zavqk")))) (properties `((upstream-name . "BgeeDB"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 6cec550e208783109f03360ec1ae347b71c5e070 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:47 +0000 Subject: gnu: r-biobtreer: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-biobtreer): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index be182a77b9..a7d6c184a2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14051,14 +14051,14 @@ anatomical terms, mapped to genes by expression patterns.") (define-public r-biobtreer (package (name "r-biobtreer") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobtreeR" version)) (sha256 (base32 - "0pynx4ps1qxsn13ba6zyg6h5dqlp2y7qish67m7sdjns079zh061")))) + "0m9gx2g5ishbbh7aqp09mpknhr7q1v5ap0s6xp6ccj01pz2gkk8s")))) (properties `((upstream-name . "biobtreeR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From b8394117f9622f0b91280e1af3cc1eedc40aef8e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:47 +0000 Subject: gnu: r-minet: Update to 3.52.0. * gnu/packages/bioconductor.scm (r-minet): Update to 3.52.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a7d6c184a2..7453e24ae9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14078,14 +14078,14 @@ mappings functionalities.") (define-public r-minet (package (name "r-minet") - (version "3.50.0") + (version "3.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minet" version)) (sha256 (base32 - "0bir2zr4r2wawkdvdhrk2hcyxmgkrkfvx36jj85fcm24axlqrzzb")))) + "0nhgvgci4r9pjfsnvxyj2q8im1wvig4zmfx2kidw8f63x2ip2rbd")))) (properties `((upstream-name . "minet"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From c14f5bd30aca61372a2b6adc7855211975ba5ce8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:48 +0000 Subject: gnu: r-genetclassifier: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-genetclassifier): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7453e24ae9..256d7e8e82 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14100,14 +14100,14 @@ information networks from data.") (define-public r-genetclassifier (package (name "r-genetclassifier") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geNetClassifier" version)) (sha256 (base32 - "1i1cavbbvxzqgqxfmikghnls18jrq12hb953mjrwa95lkhzdxm2d")))) + "1phyphdc1i55ab1a05633b0p41q8n7w0byp1plgcav2s3h8mk1km")))) (properties `((upstream-name . "geNetClassifier"))) (build-system r-build-system) -- cgit 1.4.1 From c91514edd18c2b552d21a3895fd19411155403cc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:48 +0000 Subject: gnu: r-dir-expiry: Update to 1.2.0. * gnu/packages/bioconductor.scm (r-dir-expiry): Update to 1.2.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 256d7e8e82..02e95ebc2f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14128,14 +14128,14 @@ interface to query the classifier.") (define-public r-dir-expiry (package (name "r-dir-expiry") - (version "1.0.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dir.expiry" version)) (sha256 (base32 - "05mk7iwzay1xrgvssbz7nyl5d1n03syalbk18lmjmbx05dy0cjik")))) + "1bwmlxmizhmim2l0mk406hxfr5mnmsg5zbqkjyygaipa971m9s00")))) (properties `((upstream-name . "dir.expiry"))) (build-system r-build-system) (propagated-inputs `(("r-filelock" ,r-filelock))) -- cgit 1.4.1 From fd0d1440441f99b8ae0ab741c31f40243558de7e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:48 +0000 Subject: gnu: r-basilisk-utils: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-basilisk-utils): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 02e95ebc2f..de2dbdbb87 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14152,14 +14152,14 @@ eliminating obsolete caches generated by old versions of packages.") (define-public r-basilisk-utils (package (name "r-basilisk-utils") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk.utils" version)) (sha256 (base32 - "0qbm6rj6h059hakflbwz4j4f59311jhbk5dnpx11kyixh5pgjk7v")))) + "0578rq2yz24sv7anb7vp0a0y35944ag1l8ca6haanb03wl97wm99")))) (properties `((upstream-name . "basilisk.utils"))) (build-system r-build-system) -- cgit 1.4.1 From a7a77af71a56a40fb0c144ac88f5f8e81e626545 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:48 +0000 Subject: gnu: r-basilisk: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-basilisk): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index de2dbdbb87..8a263ef9ad 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14176,14 +14176,14 @@ package, primarily for creation of the underlying Conda instance.") (define-public r-basilisk (package (name "r-basilisk") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk" version)) (sha256 (base32 - "1nzbn3f2jzvg3a3m6wgksi4cvamqas2q7csdk4ir7fcirasf536v")))) + "1cdkpngv9qybd9yxc3i2201p433vkkahs71v28x6lgs5l2wz3m1a")))) (properties `((upstream-name . "basilisk"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 79285bf0dabb7b9eff1f9a05065847b92ef8f2dd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:48 +0000 Subject: gnu: r-biocthis: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-biocthis): Update to 1.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8a263ef9ad..68f82b2022 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14204,14 +14204,14 @@ Python environments in a single R session.") (define-public r-biocthis (package (name "r-biocthis") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocthis" version)) (sha256 (base32 - "08awghsg7q22csb0j9dr8dpb1vkn9gcs9qnhhljxifkw2ahbqia4")))) + "0kh5lmv992v4r5r58x29403cll0zxr9fx4ar81nrzvnch5668v39")))) (properties `((upstream-name . "biocthis"))) (build-system r-build-system) (arguments -- cgit 1.4.1 From dbfdfecfd1c477fd7230fd97757501d23d293a21 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:48 +0000 Subject: gnu: r-biocdockermanager: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-biocdockermanager): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 68f82b2022..a3272e3ae3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14238,14 +14238,14 @@ Bioconductor-friendly.") (define-public r-biocdockermanager (package (name "r-biocdockermanager") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocDockerManager" version)) (sha256 (base32 - "0dh1flm5chsdcihljrg6znjskqkp0qyjh39hsv4zq0frf1rm97j7")))) + "1kpdmpcngnl667bfffp9bkf8c31ipmhsncq0h9bf3a4k8b83pi0w")))) (properties `((upstream-name . "BiocDockerManager"))) (build-system r-build-system) -- cgit 1.4.1 From 1503c74ce08fcfb83664a10e2f58aa1e08cb6126 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:48 +0000 Subject: gnu: r-biodb: Update to 1.2.0. * gnu/packages/bioconductor.scm (r-biodb): Update to 1.2.0. [propagated-inputs]: Add r-biocfilecache. --- gnu/packages/bioconductor.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a3272e3ae3..14f0084add 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14268,18 +14268,19 @@ the Bioconductor project.") (define-public r-biodb (package (name "r-biodb") - (version "1.0.4") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biodb" version)) (sha256 (base32 - "1apnbr5p619nsrhd2drm6arj69sw0wijv8ap7dfrndqkffrpbfmx")))) + "0q343zbx341xdy634p50k7bj6byv8v2rqzy50nw75a79206pajl4")))) (properties `((upstream-name . "biodb"))) (build-system r-build-system) (propagated-inputs - `(("r-chk" ,r-chk) + `(("r-biocfilecache" ,r-biocfilecache) + ("r-chk" ,r-chk) ("r-jsonlite" ,r-jsonlite) ("r-lgr" ,r-lgr) ("r-lifecycle" ,r-lifecycle) -- cgit 1.4.1 From 29f14a86bf1b80d0ef8fc2e9646b055ec31f65a7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:49 +0000 Subject: gnu: r-biomformat: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-biomformat): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 14f0084add..8dd5095f72 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14313,14 +14313,14 @@ separate published packages.") (define-public r-biomformat (package (name "r-biomformat") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomformat" version)) (sha256 (base32 - "1wgshkddxbmpsihpkm0dp7vqp59ns6iqbx574y80n2pxb8dx8sy9")))) + "0xf99j4lhf8kh9h1317hrbzxdv6rljs1fn68r8s40x6y4db3l817")))) (properties `((upstream-name . "biomformat"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 739c420d1e461ab4d9f4d77625dfa8b760cdd7fd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:49 +0000 Subject: gnu: r-mvcclass: Update to 1.68.0. * gnu/packages/bioconductor.scm (r-mvcclass): Update to 1.68.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8dd5095f72..54fb23a290 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14345,14 +14345,14 @@ as extensions of common core functions/methods.") (define-public r-mvcclass (package (name "r-mvcclass") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MVCClass" version)) (sha256 (base32 - "1di7y10mr7caacd6igwxnr62cm4v1x877yi4a2i5jqz1058jqni7")))) + "088gzh33vjkjf78xczqfs89pyg0k7c3533yfvijqxl84ni2ky78z")))) (properties `((upstream-name . "MVCClass"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/MVCClass") -- cgit 1.4.1 From bb98b978c3929d57c389cf8b1e06650231c66476 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:49 +0000 Subject: gnu: r-biomvcclass: Update to 1.62.0. * gnu/packages/bioconductor.scm (r-biomvcclass): Update to 1.62.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 54fb23a290..b575516c47 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14365,14 +14365,14 @@ design.") (define-public r-biomvcclass (package (name "r-biomvcclass") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioMVCClass" version)) (sha256 (base32 - "04pld93nffbci47dnf0awmcmhlfzv599ggcd7hvq78w41ac60qv8")))) + "0jqgazwz35gz11a7vzanyy2yalzalx0z0rw6y18nmk8dbv01nv2j")))) (properties `((upstream-name . "BioMVCClass"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 1086cfcb7f71df2966b0cea71c26b09569346e0c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:49 +0000 Subject: gnu: r-biomvrcns: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-biomvrcns): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b575516c47..a0a4839ff1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14390,14 +14390,14 @@ design.") (define-public r-biomvrcns (package (name "r-biomvrcns") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomvRCNS" version)) (sha256 (base32 - "0wyzj422smr4m9mswzn9inc1sn86pnia7jmd6k28nd2a7fjyrm16")))) + "01nhjhfyzs67p97bk9bjqdxk239ckl8sgfj55azk1zmw92aw2hfy")))) (properties `((upstream-name . "biomvRCNS"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 95c1308b4f1cefd72b24c68fd18f0e080ea4b781 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:49 +0000 Subject: gnu: r-bionero: Update to 1.2.0. * gnu/packages/bioconductor.scm (r-bionero): Update to 1.2.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a0a4839ff1..025fc3dd00 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14418,14 +14418,14 @@ using aCGH or sequencing.") (define-public r-bionero (package (name "r-bionero") - (version "1.0.4") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNERO" version)) (sha256 (base32 - "1yj0pavyfrj2gsvaj1dkgmznibm2appxjx9rk5qjslhslmm5b05b")))) + "0ddrzv1g46hvm52dzrcj5nbyyw9a16cqk8zg20wnkrh3qw1h4d9p")))) (properties `((upstream-name . "BioNERO"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 2aebb7bfab11b6d515f183faad6bab235bfa061c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:49 +0000 Subject: gnu: r-bionet: Update to 1.54.0. * gnu/packages/bioconductor.scm (r-bionet): Update to 1.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 025fc3dd00..87878ec6c5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14474,14 +14474,14 @@ networks.") (define-public r-bionet (package (name "r-bionet") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNet" version)) (sha256 (base32 - "15rk1jfv4h1mxvr5bs0qmq6fdnza7zcmksigqxb46fs7f6znr3yi")))) + "05rj14jn4gn0hfn57amf19b8fqwkd3y2ji3mg7m1yg1w7n4qxqsg")))) (properties `((upstream-name . "BioNet"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 73ace000f49905d4de5dbd56c261fe0825647691 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:49 +0000 Subject: gnu: r-bionetstat: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-bionetstat): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 87878ec6c5..c8eb2c969b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14507,14 +14507,14 @@ scoring subnetwork.") (define-public r-bionetstat (package (name "r-bionetstat") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNetStat" version)) (sha256 (base32 - "16xlfng9m8xvm831c2x6zmjc0gavlfiy9pnza55hdv86888fcnbg")))) + "13br8x4809hrr4ibz6iy5qjza9j6cazmkpvfikvw6bs588csxwf8")))) (properties `((upstream-name . "BioNetStat"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From b2b920b38e89538e2d03ceb9b6c253e1ede61cb6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:50 +0000 Subject: gnu: r-bioqc: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-bioqc): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c8eb2c969b..643fbbc5ae 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14549,14 +14549,14 @@ network and metabolic pathways view.") (define-public r-bioqc (package (name "r-bioqc") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioQC" version)) (sha256 (base32 - "04akp94p0d0zid55m1b1k3qlw7iq914pcg57lihgj3pa92n1sc5l")))) + "190336qk0plg79gzvfn6wfplsi8nq0nj8508g7m0w3z6bdgwy407")))) (properties `((upstream-name . "BioQC"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 494379d0151bdd93ff0bcfe2e81d75a276c392c0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:50 +0000 Subject: gnu: r-biotip: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-biotip): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 643fbbc5ae..66097bf5fd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14577,14 +14577,14 @@ optimised for high performance.") (define-public r-biotip (package (name "r-biotip") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioTIP" version)) (sha256 (base32 - "1i6r8px0fmdjx8frpljppwql74mhx08ibvhs9y3qk91ck5h3f0js")))) + "0xmy5c4i9gf6d04gara6lbnnldqmzjaascb2pd2ih60jw2mvl4ys")))) (properties `((upstream-name . "BioTIP"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From fd3a180b32e21bbc5853a62764449990e060db27 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:50 +0000 Subject: gnu: r-biotmle: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-biotmle): Update to 1.18.0. [propagated-inputs]: Remove r-dofuture and r-future. --- gnu/packages/bioconductor.scm | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 66097bf5fd..f6d853968b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14607,24 +14607,22 @@ help unravel disease regulatory trajectory.") (define-public r-biotmle (package (name "r-biotmle") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biotmle" version)) (sha256 (base32 - "01smkmbv40yprgrgi2gjnmi8ncqyrlkfdxsh33ki20amcx32nc7f")))) + "0p3iavf9059qa8qvfvqzskfc5gki3z0ivkkqdwg5anvf0wv2k47g")))) (properties `((upstream-name . "biotmle"))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) ("r-biocgenerics" ,r-biocgenerics) ("r-biocparallel" ,r-biocparallel) - ("r-dofuture" ,r-dofuture) ("r-dplyr" ,r-dplyr) ("r-drtmle" ,r-drtmle) - ("r-future" ,r-future) ("r-ggplot2" ,r-ggplot2) ("r-ggsci" ,r-ggsci) ("r-limma" ,r-limma) -- cgit 1.4.1 From 86a3ae96d1557666c8b00696a21bb4cdce6414b9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:50 +0000 Subject: gnu: r-bsseq: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-bsseq): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f6d853968b..563adeb12b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14649,14 +14649,14 @@ ensemble machine learning for the estimation of nuisance functions.") (define-public r-bsseq (package (name "r-bsseq") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bsseq" version)) (sha256 (base32 - "1xpv85hr681kkkilsnasndkszwmzbzq11y0lff4na2ilsm7sqmmi")))) + "1i30zf6457a0qd64s89x9l544y1h0hj9rfgf1m8l4krd487a9b9d")))) (properties `((upstream-name . "bsseq"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 2f03e3e1ef6b6481c9f09abadd070f54d4fc58a2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:50 +0000 Subject: gnu: r-dmrseq: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-dmrseq): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 563adeb12b..efc914f67d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14695,14 +14695,14 @@ visualizing bisulfite sequencing data.") (define-public r-dmrseq (package (name "r-dmrseq") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dmrseq" version)) (sha256 (base32 - "1jbbjifjsnk9261wqmdwkbzj1w52g6vaanpk4w816ri0fap587m4")))) + "1d6y6rbvcgprmzqkdzxg5csf0yv845d9vw10pcd1pzyndrama1vd")))) (properties `((upstream-name . "dmrseq"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 14ff65b0e8a99892bf334f4504fa325b86dcda14 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:50 +0000 Subject: gnu: r-omnipathr: Update to 3.2.0. * gnu/packages/bioconductor.scm (r-omnipathr): Update to 3.2.0. [propagated-inputs]: Add r-crayon. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index efc914f67d..7d77081754 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14741,13 +14741,13 @@ interest on transformed methylation proportions.") (define-public r-omnipathr (package (name "r-omnipathr") - (version "3.0.4") + (version "3.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OmnipathR" version)) (sha256 - (base32 "0rbq3h3cp5dgpy5ifmbnfm6z8w4jv45wjzyl1f4qacgrbyf2l30a")))) + (base32 "1q89mxnp8cig9r1499g7fb9p9x9ryz1dmc3w6ps5ww9n6rl8jqk8")))) (properties `((upstream-name . "OmnipathR"))) (build-system r-build-system) (arguments @@ -14757,6 +14757,7 @@ interest on transformed methylation proportions.") (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs `(("r-checkmate" ,r-checkmate) + ("r-crayon" ,r-crayon) ("r-curl" ,r-curl) ("r-digest" ,r-digest) ("r-dplyr" ,r-dplyr) -- cgit 1.4.1 From 76f32aae8810d1450ea5603e4060f6143fb6d7f4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:51 +0000 Subject: gnu: r-biscuiteer: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-biscuiteer): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7d77081754..ac22c2b898 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14793,14 +14793,14 @@ for ligand activity prediction from transcriptomics data.") (define-public r-biscuiteer (package (name "r-biscuiteer") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biscuiteer" version)) (sha256 (base32 - "0f4kk4v2c5diq0fbvyvgwjd1kjk9izr6n9wfrlrr7wbx4pz3c3h6")))) + "16ds322b21g8ys5c3lkrvi70i82f9rxvnknbiqx4sp6f2l01j5yj")))) (properties `((upstream-name . "biscuiteer"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 30b67fdb6a7be8d7ebb2a5efeb06bfef76ff9e0e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Nov 2021 22:04:51 +0000 Subject: gnu: r-tximeta: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-tximeta): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ac22c2b898..47bfa11e68 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14844,14 +14844,14 @@ estimates, etc.") (define-public r-tximeta (package (name "r-tximeta") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximeta" version)) (sha256 (base32 - "0ipgpcl93cac4qff6lp9x2l3gav5kb1x1d56g32h09hlm797rvvh")))) + "03fbz6pka7bcbhd0bblgckyxsqhzp4n8qp2dcpdb3sr01lyw4bc5")))) (properties `((upstream-name . "tximeta"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 55bdb2b33b0469f340b565dec147118ced314a88 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 7 Nov 2021 22:59:24 +0100 Subject: gnu: libebur128: Update to 1.2.6. * gnu/packages/audio.scm (libebur128): Update to 1.2.6. --- gnu/packages/audio.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 5b3d9f3940..15bd6e874c 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -3314,7 +3314,7 @@ Suil currently supports every combination of Gtk, Qt, and X11.") (define-public libebur128 (package (name "libebur128") - (version "1.2.4") + (version "1.2.6") (source (origin (method git-fetch) @@ -3323,7 +3323,7 @@ Suil currently supports every combination of Gtk, Qt, and X11.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0n81rnm8dm1zmibkr2v3q79rsd609y0dbbsrbay18njcjva88p0g")))) + (base32 "0xkpz5rzz1j1srhprbh89669gw8z5f1njpvcnxqgf7qax69vd8sh")))) (build-system cmake-build-system) (arguments `(;; Tests require proprietary .wav files. See -- cgit 1.4.1 From e46e144b42c2c95dcebedb0007b722032ff93c28 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 7 Nov 2021 23:15:25 +0100 Subject: gnu: redkite: Update to 1.3.1. * gnu/packages/audio.scm (redkite): Update to 1.3.1. --- gnu/packages/audio.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 15bd6e874c..5e274f36d8 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -4918,7 +4918,7 @@ workstations as well as consumer software such as music players.") (define-public redkite (package (name "redkite") - (version "1.3.0") ;marked unmaintained as of Oct. 2021 + (version "1.3.1") ;marked unmaintained as of Oct. 2021 (source (origin (method git-fetch) @@ -4927,7 +4927,7 @@ workstations as well as consumer software such as music players.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "16j9zp5i7svq3g38rfb6h257qfgnd2brrxi7cjd2pdax9xxwj40y")))) + (base32 "1zb2k2a4m7z2ravqrjn8fq8lic20wbr2m8kja3p3113jsk7j9zvd")))) (build-system cmake-build-system) (arguments `(#:tests? #f)) ;no tests included -- cgit 1.4.1 From e568b14076aacfc6a46b718bb930070fb77d70eb Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 8 Nov 2021 01:03:46 +0100 Subject: gnu: hplip: Update to 3.21.10. * gnu/packages/cups.scm (hplip): Update to 3.21.10. [snippet]: Make substitution patterns more specific. [arguments]: Don't explicitly return #t from phases. --- gnu/packages/cups.scm | 27 +++++++++++++-------------- 1 file changed, 13 insertions(+), 14 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cups.scm b/gnu/packages/cups.scm index e4ae35d8ae..1c86ef561c 100644 --- a/gnu/packages/cups.scm +++ b/gnu/packages/cups.scm @@ -490,14 +490,14 @@ should only be used as part of the Guix cups-pk-helper service.") (define-public hplip (package (name "hplip") - (version "3.21.8") + (version "3.21.10") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/hplip/hplip/" version "/hplip-" version ".tar.gz")) (sha256 (base32 - "076fjzgw86q817c660h1vzwdp00cyjr49b9bfi7qkhphq6am4gpi")) + "0q3adcp8iygravp4bq4gw14jk20c5rhnawj1333qyw8yvlghw8yy")) (modules '((guix build utils))) (snippet '(begin @@ -512,9 +512,13 @@ should only be used as part of the Guix cups-pk-helper service.") (delete-file "prnt/hpcups/ImageProcessor.h") (substitute* "Makefile.in" ((" -lImageProcessor ") " ") - (("(\\@HPLIP_BUILD_TRUE\\@[[:blank:]]*).*libImageProcessor.*" + ;; Turn shell commands inside an if…fi into harmless no-ops. + (("^(\\@HPLIP_BUILD_TRUE\\@[[:blank:]]*).*libImageProcessor.*" _ prefix) - (string-append prefix ":; \\\n"))) + (string-append prefix ": ; \\\n")) + ;; Remove the lines adding file targets altogether. + (("^\\@FULL_BUILD_TRUE\\@.*libImageProcessor.*") + "")) ;; Install binaries under libexec/hplip instead of ;; share/hplip; that'll at least ensure they get stripped. @@ -523,8 +527,7 @@ should only be used as part of the Guix cups-pk-helper service.") (("^dat2drvdir =.*") "dat2drvdir = $(pkglibexecdir)\n") (("^locatedriverdir =.*") - "locatedriverdir = $(pkglibexecdir)\n")) - #t)))) + "locatedriverdir = $(pkglibexecdir)\n")))))) (build-system gnu-build-system) (outputs (list "out" "ppd")) (home-page "https://developers.hp.com/hp-linux-imaging-and-printing") @@ -613,8 +616,7 @@ should only be used as part of the Guix cups-pk-helper service.") (string-append "rulessystemdir = " out "/lib/systemd/system")) (("/etc/sane.d") - (string-append out "/etc/sane.d"))) - #t))) + (string-append out "/etc/sane.d")))))) (add-before 'configure 'fix-build-with-python-3.8 (lambda* (#:key inputs #:allow-other-keys) (let ((python (assoc-ref inputs "python"))) @@ -625,15 +627,13 @@ should only be used as part of the Guix cups-pk-helper service.") (setenv "C_INCLUDE_PATH" (string-append python "/include/python" (python:python-version python) - ":" (getenv "C_INCLUDE_PATH")))) - #t))) + ":" (getenv "C_INCLUDE_PATH"))))))) (add-after 'install 'install-models-dat (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (models-dir (string-append out "/share/hplip/data/models"))) - (install-file "data/models/models.dat" models-dir)) - #t)) + (install-file "data/models/models.dat" models-dir)))) (add-after 'install 'wrap-binaries ;; Scripts in /bin are all symlinks to .py files in /share/hplip. ;; Symlinks are immune to the Python build system's 'WRAP phase, @@ -664,8 +664,7 @@ should only be used as part of the Guix cups-pk-helper service.") bin target))) (chmod file #o755))) (find-files "." (lambda (file stat) - (eq? 'symlink (stat:type stat))))) - #t))))))) + (eq? 'symlink (stat:type stat)))))))))))) ;; Note that the error messages printed by the tools in the case of ;; missing dependencies are often downright misleading. -- cgit 1.4.1 From 551047838d7c6cf1ac3777b20b38b5e047f54832 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 8 Nov 2021 01:11:15 +0100 Subject: gnu: knot: Update to 3.1.4. * gnu/packages/dns.scm (knot): Update to 3.1.4. --- gnu/packages/dns.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm index 0aaa22bbfd..b289aa999e 100644 --- a/gnu/packages/dns.scm +++ b/gnu/packages/dns.scm @@ -923,7 +923,7 @@ Extensions} (DNSSEC).") (define-public knot (package (name "knot") - (version "3.1.3") + (version "3.1.4") (source (origin (method git-fetch) @@ -932,7 +932,7 @@ Extensions} (DNSSEC).") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "19hm17r6v8p9k3jp3bkj4xzjrb8irfmpgz6mjad5gfhmgr4pmi51")) + (base32 "0wx8ad95adryzp527m4k0lja8y39qqd65f5z9immhfpb9cyax6i7")) (modules '((guix build utils))) (snippet '(begin -- cgit 1.4.1 From 3f4eb02fe523f63eaf5c44e323f77061977aba7d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 8 Nov 2021 01:21:05 +0100 Subject: gnu: fheroes2: Update to 0.9.9. * gnu/packages/games.scm (fheroes2): Update to 0.9.9. --- gnu/packages/games.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index f33ee8795b..a474933c93 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -12686,7 +12686,7 @@ disassembly of the DOS version, extended with new features.") (define-public fheroes2 (package (name "fheroes2") - (version "0.9.8") + (version "0.9.9") (build-system cmake-build-system) (arguments `(#:tests? #f ; no tests @@ -12706,7 +12706,7 @@ disassembly of the DOS version, extended with new features.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1sc7rmyiciahxh5f6rarhil2hrw8q8sjdssh063grji50mlnrf6a")))) + (base32 "030kfaagxy3i7bjvbx2nf05jmbbh5g2r52l17y9bl6vbfj67yvxy")))) (home-page "https://ihhub.github.io/fheroes2/") (synopsis "Turn-based strategy game engine") (description "@code{fheroes2} is an implementation of Heroes of Might and -- cgit 1.4.1 From 805ca61eb9681ccd0287d4d80178b888b85da874 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 8 Nov 2021 02:05:23 +0100 Subject: gnu: nginx: Update to 1.21.4. * gnu/packages/web.scm (nginx): Update to 1.21.4. --- gnu/packages/web.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index d7df3079b3..847bf88118 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -368,18 +368,18 @@ the same, being completely separated from the Internet.") (define-public nginx (package (name "nginx") + ;; Please update the nginx-documentation package together with this one! ;; Track the ‘mainline’ branch. Upstream considers it more reliable than ;; ’stable’ and recommends that “in general you deploy the NGINX mainline ;; branch at all times” (https://www.nginx.com/blog/nginx-1-6-1-7-released/) - ;; Please update the nginx-documentation package together with this one! - (version "1.21.3") + (version "1.21.4") (source (origin (method url-fetch) (uri (string-append "https://nginx.org/download/nginx-" version ".tar.gz")) (sha256 (base32 - "0nhps7igdqcpcy1r8677ar807rfclpylmz3y858a678m1np4lxql")))) + "1ziv3xargxhxycd5hp6r3r5mww54nvvydiywcpsamg3i9r3jzxyi")))) (build-system gnu-build-system) (inputs `(("libxml2" ,libxml2) ("libxslt" ,libxslt) -- cgit 1.4.1 From 9d25ee30b188f9202cc14f7cd25ba8a1c3ec1a72 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 8 Nov 2021 02:05:40 +0100 Subject: gnu: nginx-documentation: Update to 1.21.4-2791-9385526a9b2d. * gnu/packages/web.scm (nginx-documentation): Update to 1.21.4-2791-9385526a9b2d. --- gnu/packages/web.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 847bf88118..fb0ca7646a 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -474,9 +474,9 @@ and as a proxy to reduce the load on back-end HTTP or mail servers.") (define-public nginx-documentation ;; This documentation should be relevant for the current nginx package. - (let ((version "1.21.3") - (revision 2769) - (changeset "16f6fa718be2")) + (let ((version "1.21.4") + (revision 2791) + (changeset "9385526a9b2d")) (package (name "nginx-documentation") (version (simple-format #f "~A-~A-~A" version revision changeset)) @@ -488,7 +488,7 @@ and as a proxy to reduce the load on back-end HTTP or mail servers.") (file-name (string-append name "-" version)) (sha256 (base32 - "1rjq5xqzx843yk9nblz8lq14r4kmlrahap7m0lkvx5mky80vqp79")))) + "07v5vpwg2k4y1asbygmrvsk61l1vbdb2pyllc5k4hcjykg9avfza")))) (build-system gnu-build-system) (arguments '(#:tests? #f ; no test suite -- cgit 1.4.1